|
Virus Name |
Crystal conditions/Reference |
Φ-X 174 DNA binding protein J
(1rb8) |
Crystals (of chimera virion) were obtained in sitting drops by incubation after combining an equal volume of virus sample at 6.7 mg/ml with well solution (4–7% (w/v) PEG8000, 100 mM sodium citrate (pH 5.0), 40% (v/v) glycerol, 0.02% (w/v) sodium azide, 0.1% (v/v) β-mercaptoethanol, 0.9 M NaCl) after incubation at 45 °C overnight. The chimeric α3 crystals were stable at 25 °C and could be stored at room temperature prior to data collection.
Reference: 15046981 |
Adeno-Associated Virus
(1lp3) |
Crystallization was by vapor diffusion with AAV at approx. 8.5 mg/ml in 25% glycerol, equilibrated against a reservoir also containing 4-5% polyethylene glycol 6000.
Reference: 12136130 |
Alfalfa Mosaic Virus
(amv) |
Crystallization was performed in dialysis cells containing about 0.05 ml of solution containing 12 mg of AMV-protein/ml in 0.05 M-pyrophosphate buffer at pH 7.0. This was dialyzed against 0.2 M-citrate buffer at pH 4.6. Two types of crystals were formed even within the same cell, although type I hexagonal plates were predominant.
Reference: 7299819 |
Avian infectious bursal disease virus
(1wce) |
No information available |
Avian Infectious bursal disease virus, sub-viral particle
(1wcd) |
The IBDV SVP (Avian Infectious bursal disease virus, sub-viral particle) crystallized in three crystal forms under the following conditions: form I in 16%–24% PEG 400, 50 mM sodium acetate (pH 5); form II under the same conditions as form I but adding 50–150 mM NaCl; form III in 3%–8% PEG 8000, 100 mM Tris (pH 8). The IPNV SVP crystals grew from 1 M 1,6-hexanediol, 10 mM CoCl2, 100 mM sodium acetate (pH 4.6). For data collection at 100 K, form II crystals were transferred progressively to a cryoprotecting solution containing the same buffer and 28% PEG 400 plus 20% methyl-pentanediol (MPD) before flash cooling.
Reference: 15797378 |
B19 Parvovirus Capsid
(1s58) |
The capsids were crystallized by using the hanging drop vapor diffusion technique. Aliquots (1.5 μl) of the purified capsid (9 mg·ml–1 in 10 mM Tris·HCl, pH 7.5) were mixed with an equal volume of reservoir solution (16–22% 2-methyl-2,4-pentanediol in 0.1 M sodium cacodylate buffer, pH 7.4), and the droplets were equilibrated against 750 μl of reservoir solution at 20°C.
Reference: 15289612 |
Bacteriophage α3
(1m06) |
The virion was crystallized by vapor diffusion using sitting drops at 45 °C. A 10 μl drop of sample was mixed with an equal volume of reservoir buffer containing 3–5% PEG 8000, 100 mM sodium citrate (pH 5.0), 40% (v/v) glycerol, 0.02% sodium azide, and 0.1% β-mercaptoethanol.
Reference: 12473449 |
Bacteriophage α3
(1m0f) |
No information available |
Bacteriophage Φ-X 174
(2bpa) |
Crystals grown with hanging drop vapor diffusion method using PEG 8000 as precipitant. The reservoir solution contained 90 to 93 mM bis-TRIS methane at pH 6.8 and 1.5 to 2.0% ((W/V) PEG 8000. The hanging drop contained a mixture of 5 µl of virus solution (40 µg of virus) and 5 µl of reservoir solution. The reservoir was filled with 500 µl of solution. The hanging drops were kept at room temperature for 1 to 2 weeks and then transferred to the cold room at 4 ° C for another 2 or more weeks.
Reference: 1418820 |
Bacteriophage FR (4 Residue Deletion FG Loop)
(1fr5) |
No information available |
Bacteriophage FR (FR)
(1frs) |
Crystals grown by hanging drop vapor diffusion method with 10 µl drops containing 25 mg protein/ml and 10% saturated ammonium sulfate in 50 mM MOPS (pH 7.5) 0.02% NaN3 equilibrated against 35% saturated ammonium sulfate in the same buffer system.
Reference: 7966339 |
Bacteriophage G4
(1gff) |
The procapsid particles were crystallized at room temperature using the hanging drop vapor diffusion method. The reservoir solution contained 2.0% (W/V) PEG 8000 and 0.2 M KCl in 50 mM bis-TRIS (pH 6.8) buffer, over which was suspended a hanging drop of 5 µl of reservoir solution. Large amount of precipitation were observed forming around the growing crystals, which started to appear approx. two weeks after crystal trays were set up. It was shown, using SDS/polyacrylamide gel electrophoresis, that during the crystallization process the scaffolding proteins B and D dissociated from the procapsid particles and precipitated, leaving the degraded particles to crystallize.
Reference: 8642594 |
Bacteriophage GA Protein Capsid (GA)
(1gav) |
The crystallization experiments were carried out in hanging drops by the vapor diffusion technique at room temperature (20 ° C). The solution in the crystallization drop was prepared by mixing 10 µl of phage solution with 10 µl of 5% ammonium sulfate in 0.04 M TRIS-HCl (pH 8.0), 0.15 M NaCl and 0.02% NaN3. The droplets were equilibrated against 0.9 M NaCl in 0.04 M TRIS-HCl (pH 8.0). Crystals with a size of 0.6 mm were obtained in three weeks.
Reference: 9299325 |
Bacteriophage HK97 Mature Empty Capsid
(1ohg) |
The initial crystallization conditions were identified by hanging drop vapor diffusion. The initial drop volumes ranged between 2 and 8
Reference: 9527920 |
Bacteriophage MS2 (MS2)
(2ms2) |
Crystallization experiments were performed in hanging drops by vapor diffusion technique at 37 ° C, 19 ° C and 4 ° C. Crystals were grown in 20 µl droplets applied to the inside of the lid of sterile plastic Petri dish. The virus solution contained 1.0% (W/V) MS2, 0.2 M sodium phosphate (pH 7.4) 1.5% (W/V) NaN3. The droplets were equilibrated against 0.4 M sodium phosphate (pH 7.4).
Reference: 1772631 |
Bacteriophage MS2 Mutant (T45A)/RNA Operator
(1aq4) |
No information available |
Bacteriophage MS2 Mutant (T59S)/RNA Operator
(1aq3) |
No information available |
Bacteriophage MS2 Mutant T45A
(1mva) |
No information available |
Bacteriophage MS2 Mutant T59S
(1mvb) |
No information available |
Bacteriophage MS2, Mutant E76D
(1mst) |
No information available |
Bacteriophage MS2, Mutant P78N
(1bms) |
No information available
Reference: 8594200 |
Bacteriophage MS2/19 nt. MS2 RNA Fragment
(1zdh) |
Crystals of the recombinant capsids were grown by vapour diffusion from hanging drops containing 0.6 mg ml−1 capsid, 1.25% (w/v) polyethyleneglycol 8000 in 0.1 M sodium phosphate (pH 7.4) and 0.02% (w/v) sodium azide. The droplets were equilibrated against a solution containing 0.4 M sodium phosphate (pH 7.4) and 0.02% (w/v) sodium azide at 37°C. Rhombohedral crystals appeared after one to three weeks with dimensions up to 1.5 mm. Crystals of the recombinant capsid were soaked with these (wild type and C-5 variant) two synthetic RNA fragments.
Reference: 9245600 |
Bacteriophage MS2/19 nt. MS2 RNA Fragment
(1zdi) |
Same as for PDB ID:1zdh
Reference: 9245600 |
Bacteriophage MS2/23 nt. MS2 RNA Fragment
(1zdk) |
No information available |
Bacteriophage MS2/8 nt. MS2 RNA Fragment
(1zdj) |
No information available
Reference: 9917072 |
Bacteriophage MS2/RNA Aptamer F5
(5msf) |
No information available
Reference: 9245600 |
Bacteriophage MS2/RNA Aptamer F5 (2-aminopurine at -10 pos.)
(1u1y) |
Crystals of MS2 capsids, free of native RNA, were grown using previously described crystallization conditions (Valegård et al. 1986 J. Mol. Biol. 190: 587–591) and the hanging drop technique of vapor diffusion. Crystals were up to 1.5 mm (largest dimension) in size, having space group R32 with cell dimensions a = b = 288.0 Å and c = 653.0 Å. The crystals were soaked with the F5/2AP10 RNA (F5 aptamer RNA stem-loop with 2AP substituted at the −10 position), at a final concentration of 2 mg/mL, for 5 d prior to mounting in glass capillaries for data collection.
Reference: 15496523 |
Bacteriophage MS2/RNA Aptamer F6
(6msf) |
No information available
Reference: 9245600 |
Bacteriophage MS2/RNA Aptamer F7
(7msf) |
No information available
Reference: 9245600 |
Bacteriophage MS2/RNA Hairpin (2One-5)
(1e7x) |
No information available |
Bacteriophage MS2/RNA Hairpin (2Thio-U-5)
(1he0) |
No information available |
Bacteriophage MS2/RNA Hairpin (2Thio-U-5-6)
(1hdw) |
No information available |
Bacteriophage MS2/RNA Hairpin (4One-5)
(1dzs) |
No information available |
Bacteriophage MS2/RNA Hairpin (5Bru-5)
(1e6t) |
No information available |
Bacteriophage MS2/RNA Hairpin (5bru-5) Complex
(2bu1) |
The MS2 capsids, free of native RNA was crystallized as described in Valegard et al (1986) J.Mol.Biol., 190:587-591. The crystals were soaked with the different RNAs to a final concentration of 3mg/ml for four to seven days and thereafter mounted in glass capillaries prior to datacollection.
Reference: 11720290 |
Bacteriophage MS2/RNA Hairpin (Ade-5)
(1he6) |
No information available |
Bacteriophage MS2/RNA Hairpin (C-10)
(1kuo) |
No information available |
Bacteriophage MS2/RNA Hairpin (C-7)
(1gkv) |
No information available |
Bacteriophage MS2/RNA Hairpin (G-10)
(1gkw) |
No information available |
Bacteriophage MS2/RNA Hairpin (G-5)
(1h8j) |
No information available |
Bacteriophage PP7
(1dwn) |
Crystals were obtained under two different conditions using the hanging-drop technique. In both cases, 5 µl of phage solution (7 mg/ml) was mixed with an equal volume of reservoir solution. Crystal type A (irregular shape) was obtained using 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5 and 30%(V/V) 2-methyl-4,4-pentanediol at room temperature. Crystal types B and C (rhombic shape) were obtained using 0.1 M sodium citrate buffer pH 5.6 and 3.0 M 1,6-hexanediol at 310 K. Crystal form A grew to a maximum dimension of 1 mm in about two weeks. Crystal forms B and C grew to a size of 1.8 mm in about six weeks.
Reference: 10739912 |
Bacteriophage PRD1
(1w8x) |
The virus preparation was used undiluted, with concentrations ranging from 7 to 20 mg.ml-1. The virus was fixed using 0.025%(w/v) gluteraldehyde immediately after the final anion-exchange chromatography step and crystallizations were set up 15 min after glutaraldehyde addition. A 3 µl volume of the virus and precipitant solution was injected into a thin-walled quartz capillary 15 mm in length and 0.5 mm in diameter. The capillary was then fixed to a sitting-drop microbridge using Plasticine and the assembly placed into the well of a sitting-drop tray. The mother liquor was equilibrated against 1 ml of reservoir solution by vapour diffusion via the open ends of the capillary. The conditions for crystallization were derived from those used for sitting drops (Bamford (2002) J.Mol.Biol. 139:103-112). The solution inside the capillary tube was a 1:1 mix of the virus solution described above with a solution of 3.7-4.3%(w/v) PEG 8000, 400 mM NaCl and 100 mM potassium phosphate buffer pH 7.2 as precipitant. The reservoir solution consisted of 16-20% PEG 8000 with salt and buffer as above.
Reference: 12595719 |
Bacteriophage Prd1 Sus1 Mutant
(1hb7) |
No information available |
Bacteriophage Qβ Capsid (QB)
(1qbe) |
Crystals grown by hanging drop vapor diffusion method at room temperature. The solution in the crystallization well was prepared by mixing 12 µl of virus solution (10 mg/ml) with 8 µl of 2% PEG 6000 in 0.05 M TRIS/HCl pH 7.4, 0.2 M NaCl, 0.1 mM MgSO4, 0.01 mM EDTA and 0.02% (W/V) NaN3. The droplets were equilibrated against 0.4 M NaCl.
Reference: 8736553 |
Bean Pod Mottle Virus, Middle Component
(1pgl) |
No information available
Reference: 2749253 |
Bean Pod Mottle Virus, Top Component
(1pgw) |
No information available |
Black Beetle Virus (BBV)
(2bbv) |
Crystals grown at 20 ° C using hanging drop vapor diffusion method. A virus solution was prepared at 8 mg/ml using sodium phosphate buffer in a pH range of 6.9 to 7.2. The reservoir solution contained 0.55 M ammonium sulfate in 0.05 M sodium phosphate buffer adjusted to the same pH as the solution containing the virus. 5 µl of virus solution were mixed with 5 µl of reservoir solution and the mixture was equilibrated with 1 ml of the reservoir solution. The crystals would grow more rapidly if the reservoir and virus solution were initially made 1 and 0.5% (W/V) respectively in PEG 8000. |
Bluetongue Virus
(2btv) |
Crystallization trials (for BTV 1SA) were carried out by vapor diffusion (sitting drop) using microbridges supplied by Crystal Microsystems. The precipitant solution in the reservoir ranged from 11 to 16% saturated ammonium sulfate in 0.1 M TRIS-HCl buffer, pH 8.0. In some trials 15% ethylene glycol was also included in the reservoir solution. Usually 10 µl of treated cores were mixed with 5 µl reservoir solution. Regular crystals grow with the morphology of half rhombic dodecahedra, to a diameter of 0.3 mm in approx. 4 weeks and then more slowly to a maximum diameter of 0.8 mm. The largest crystals, though fewer in number, were obtained together with noncrystalline aggregates, when ethylene glycol was incorporated in the reservoir solution.
Reference: 9774103 |
Bovine Enterovirus VG-5-27
(1bev) |
Purified virus was suspended at a concentration of 10 mg/ml in 20 mM TRIS.HCl (pH 7.6) containing 50 mM NaH2PO4 and 0.75% (V/V) saturated ammonium sulfate. Then the suspended virus was placed in 10 µl dialysis buttons, sealed with untreated Visking tubing and submerged in mother liquor consisting of 100 mM NaH2PO4 (pH 7.6) and various quantities of saturated ammonium sulfate in the range 20% to 35% (V/V). Crystallizations were incubated at 20 ° C. all solutions contained sodium azide at trace concentrations to inhibit microbiological growth during the experiments.
Reference: 8390580 |
Brome Mosaic Virus
(1js9) |
Rhombohedral BMV crystals were obtained by mixing 10 μl of virus solution with 10 μl of 23% polyethylene glycol 550 mono-methyl ether containing 0.1 M magnesium acetate at pH 5.2. The drops were then equilibrated at 18°C by vapor diffusion with 1.0 ml reservoirs in Cryschem plates (Hampton Research, Laguna Niguel) sealed with clear plastic tape. Crystals were visible after about seven days and grew to about 1 mm×1.5 mm in 10–15 days.
Reference: 11916381 |
Canine Panleukopenia Virus
(1c8d) |
Virus equilibrated in 20 mM Bis-Tris (either pH 5.5 or 6.2) or against 20 mM Tris-HCl (pH 7.5) at a concentration of 10 mg/ml. Sitting drop crystallizations were set up in microbridges (Hampton Research, Laguna Niguel, CA, USA) by adding 5 μl of virus suspension to 5 μl of mother liquor, which contained 0.75% to 1.50% (w/v) PEG 8000 and either 8 mM CaCl2 or 5 mM EDTA. The bridges were placed in the wells containing 0.5 ml of mother liquor at the same pH as the drop. The wells were sealed with clear tape and incubated at 19°C for 2-5 months.
Reference: 10884355 |
Canine Parvovirus
(2cas) |
Both CPV full and empty particles were crystallized using the hanging drop method in TRIS-HCl buffer at pH 7.5 containing 0.75% PEG 8000 and 8 mM CaCl2. |
Canine Parvovirus
(1p5y) |
See xtal conditions for PDB ID: 1p5w
Reference: 14581558 |
Canine Parvovirus
(1p5w) |
Crystals of empty particles of CPV-N93D (PDB ID: 1p5y) and full DNA containing particles of CPV-N93R (PDB ID: 1p5w) were grown at 20°C with 1% PEG 8000 and 8 mM CaCl2 in 20 mM Tris-HCl (pH 7.5) by using the sitting-drop vapor diffusion technique. The crystals were cryoprotected with 30% (vol/vol) ethylene glycol and 5% PEG 8000 in 20 mM Tris-HCl (pH 7.5) containing 8 mM CaCl2 and then flash frozen in liquid nitrogen vapor prior to data collection.
Reference: 14581558 |
Canine Parvovirus Strain D
(4dpv) |
No information available
Reference: 8969301 |
Canine Parvovirus Strain D (pH 5.5)
(1c8h) |
Virus equilibrated in 20 mM Bis-Tris (either pH 5.5 or 6.2) or against 20 mM Tris-HCl (pH 7.5) at a concentration of 10 mg/ml. Sitting drop crystallizations were set up in microbridges (Hampton Research, Laguna Niguel, CA, USA) by adding 5 μl of virus suspension to 5 μl of mother liquor, which contained 0.75% to 1.50% (w/v) PEG 8000 and either 8 mM CaCl2 or 5 mM EDTA. The bridges were placed in the wells containing 0.5 ml of mother liquor at the same pH as the drop. The wells were sealed with clear tape and incubated at 19°C for 2–5 months.
Reference: 10884355 |
Canine Parvovirus Strain D, Mutant A300D
(1ijs) |
Crystals were grown using the hanging drop vapor diffusion method with the same conditions as had been used to crystallize wild-typeCPV
Reference: 8918534 |
Carnation Mottle Virus
(1opo) |
Crystals were obtained in 40 µl droplets of 0.1 M TRIS-HCl buffer solution containing 40-50 mg/ml of virus and 10% saturated ammonium sulfate. The equilibrating solution consisted of 0.1 M TRIS-maleic (mal)/NaOH, pH 5.03 with 25% saturated ammonium sulfate. Either 1.7 heptandiol or PEG 300 were added to lessen the number of pellets.
Reference: 8307192 |
CCMV Swollen Form Model 1
(ccmv_swln_1) |
No information available |
CCMV Swollen Form Model 2
(ccmv_swln_2) |
No information available |
Cocksfoot Mottle Virus
(1ng0) |
Crystals were obtained under two different conditions using the hanging drop technique. In both cases, 5 µl of virus solution (10 mg/ml) were mixed with an equal volume of bottom solution. Crystal type A (irregular, cucumber-like shape) was obtained using 0.25 M sodium succinate buffer at pH 3.3 and 5% PEG 8000 as an additive. Crystal type B (prism) was obtained using 0.1 M sodium phosphate buffer, pH 5.5, and 2 M NaCl as precipitant. Crystal form A belonged to orthorhobic space group (: structure reported) and crystal from B belonged to tetragonal space group.
Reference: 12781716 |
Cowpea Chlorotic Mottle Virus (CCMV)
(1cwp) |
Crystallized by the sitting drop vapor diffusion method. The reservoir buffer was 0.3 M disodium succinate, 0.3 M succinic acid, 1 mM sodium azide, 3.7-4.0% PEG 8000, pH 3.3. Each droplet consisted of 5-25 µl of virus at 20-50 mg/ml in storage buffer, added to an equal volume of reservoir buffer. The dishes were sealed and allowed to equilibrate at room temperature in darkness against 15 ml of reservoir buffer.
Reference: 8438568 |
Cowpea Mosaic Virus
(1ny7) |
Cubic crystals displaying rhombic dodecahedral morphology were obtained by vapor diffusion. The reservoir solution was 0.4 M ammonium sulfate, 2% PEG 8000 (W/V), and 0.05 M potassium phosphate at pH 7.0. The virus solution was prepared at 35 mg/ml in 0.05 M potassium phosphate, pH 7.0.
Reference: 10603314 |
Coxsackievirus A9
(1d4m) |
No information available
Reference: 10647183 |
Coxsackievirus B3 Coat Protein
(1cov) |
Crystals grown at room temperature using the sitting drop vapor-diffusion method. The sitting drop contained 10 µl of 5mg/ml in 50 mM MES buffer, pH 6.0 with 0.75 M NaCl and the well contained 1 ml 2M ammonium sulfate. |
Cricket Paralysis Virus
(1b35) |
Crystals were grown by hangingdrop vapor-diffusion at room temperature. Drops consisted of 1 µl of well solution plus 1 µl virus at a concentration of 10 mg/ml in 200 mM NaHPO4, pH 7.2. The well solution was 8% (W/V) MPEG 5000, 50 mM lithium sulfate, 50 mM MES, pH 6.0.
Reference: 10426956 |
Cucumber Mosaic Virus (CMV)
(1f15) |
Crystals were grown using vapor diffusion and the sitting-drop method. The reservoir contained 2 M sodium formate, 0.1 M sodium acetate buffer (pH 4.6), and 0.05 to 0.125% polyethylene glycol (PEG) 8000. To the sitting drop, 10 µl of this solution was added to 8 µl of the virus solution and 2 µl of a 24 mM (10 times the critical micelle concentration) solution of CYMAL-5 (cyclohexyl-pentyl--D-maltoside) was then added. The detergent improved crystal size by decreasing the number of nucleation sites. It did not improve diffraction resolution. To prepare the crystals for freezing, drops that did not have usable crystals were pooled and centrifuged to remove precipitate. This solution was then used to make 10, 20, and 30% solutions of PEG 400. The crystals were transferred to the increasing PEG solutions, with 0.5-h incubations at each step. The crystals were then frozen in a liquid nitrogen stream that was at 110 K.
Reference: 10906212 |
Densovirus from Galleria Mellonella
(1dnv) |
10 mM TRIS pH7.5, 1mM Ca2+, 1mM Mg2+, 0.1M NaCl, 5% PEG 8000, (soaked in 25% glycerol for 4 hours as cryo-protectant)
Reference: 9817847 |
Desmodium Yellow Mottle Virus (DYMV)
(1ddl) |
Purified DYMV at a concentration of 3 mg/ml was used to screen for crystals using Crystal Screen and Crystal Screen II (Hampton Research, Laguna Hills, CA). Trials were deployed using Cryschem Plates (Charles Supper Co., Natick, MA) covered with clear tape and maintained at room temperature. Each trial used a 0.5 ml reservoir and 3 µl each of the buffer and the DYMV concentrate. Small cuboidal crystals were observed after one month with 2.0 M sodium formate (NaCHO2, Fluka), 0.1 M sodium acetate (NaC2H3O2) at pH 4.6. By optimizing the conditions, large crystals, up to 0.7 mm on a side, were grown using either the sitting or the hanging-drop method (McPherson, 1999). The pH optimum was found to be 4.8 in both cases, while the optimum sodium formate concentration ranged from 1.8-2.5 M for the hanging-drop, or 2.0-2.2 M for the sitting-drop method. Crystals were first observed after one month but continued to grow up to six months. An average drop contained three to瑬seven crystals. The cubic crystals were robust and easily manipulated with little damage from handling.
Reference: 10966774 |
Echovirus 1 (FAROUK Strain)
(1ev1) |
Virus was crystallized by microdialysis against 10mM PIPES, 25mM CaCl2, 25mM MgCl2, 2.5% PEG 400, pH 6.0 at 4 Crystals grown at 20 ° C.
Reference: 10089503 |
Echovirus 11 (Strain 207)
(1h8t) |
EV11-207 stocks were concentrated to approx. 10 mg/ml and crystallized by equilibrating 2 µl sitting drops (1 µl of virus plus 1 µl of mother liquot sealed in Linbro plates. Crystals suitable X-ray diffraction data grew in 2.0 M ammonium sulfate.
Reference: 12097583 |
Feline Panleukopenia Virus
(1c8g) |
A crystal of FPV grown at pH 7.5 was soaked for ten minutes in 20 mM Bis-Tris buffer (pH 6.2) containing 5% (w/v) PEG 8000 and 8 mM CaCl2, as well as 30% (v/v) ethylene glycol as a cryo-protectant.
Reference: 10884355 |
Feline Panleukopenia Virus
(1fpv) |
Useful crystals were obtained for both full and empty particles at room temperature, with PEG 8000 as precipitant. The reservoir solution contained 0.75% (W/V) PEG 8000 and 8 mM CaCl2 in 10 mM TRIS-HCl (pH 7.5) buffer, over which was suspended a hanging drop of 5 µl of virus diluted by 5 µl of reservoir solution. Crystals grew in a period of 2 weeks or longer.
Reference: 8392729 |
Feline Panleukopenia Virus
(1c8f) |
No information available |
Feline Panleukopenia Virus
(1c8e) |
A crystal of FPV was grown in 20 mM Bis-Tris-HCl (pH 6.2), in the presence of 5 mM EDTA.
Reference: 10884355 |
Flock House Virus
(fhv) |
FHV was crystallized by sitting-drop vapor diffusion. The reservoir buffer was 0.01 M bis(2-hydroxyethyl)iminotris(hydroxymethyl) methane (Bis-Tris), 0.02 M CaCI2, 2.8%(w/v) polyethylene glycol (PEG), molecular weight 8000, pH 6.0. The drop consisted of 10 i~1 FHV at 18 mg.ml -1 in 0.01 M Tris.HCI pH 7.2, plus 10-30 u1 of reservoir buffer. The dish was sealed and allowed to equilibrate against 13 ml of reservoir buffer at room temperature.
Reference: 1418822 |
Foot and Mouth Disease Virus
(1qqp) |
Crystals of FMDV O1BFS (space group I23, a 5 345 Å) were grown using ammonium sulfate as precipitant (Fox et al., 1987). Crystals were soaked in 3 kDa/6 kDa heparin or HS (in the form of a sodium salt from Sigma) at a concentration of 20 mg/ml, pH 7.5 for at least 4 h prior to mounting in quartz capillaries. For some crystals, the mother liquor was exchanged for 30% PEG 4K prior to soaking and other crystals were treated with DTT (Logan et al., 1993) to permit ordering of the integrin receptor attachment site (the VP1 G–H loop). Crystals of O1K also grown from ammonium sulfate (Curry et al., 1992) were soaked with 20 mg/ml 6 kDa heparin.
Reference: 9927414 |
Foot and Mouth Disease Virus (FMDV)
(1bbt) |
Purified virus was crystallized either by dialysis in 5 to 100 µl of ammonium sulfate in 0.1 M sodium phosphate (pH 7.6), containing a trace of NaN3 as a preservative or in vapor diffusion chambers in which the virus droplet had been diluted with an equal volume of the ammonium sulfate solution in the reservoir. All crystallizations were carried out at the room temperature.
Reference: 8382928 |
Foot and Mouth Disease Virus (Reduced)
(1fod) |
No information available |
Foot and Mouth Disease Virus Type C-S8C1
(1fmd) |
Crystals of FMDVs C-S8c1 and SD6-6 grew by vapour diffusion from 9.5–11.5 % saturated (NH 4) 2SO 4in the presence of 10 mM dithiothreitol
Reference: 8081743 |
Human Adenovirus 2 Penton Base
(1x9p) |
Crystals were grown in hanging drops against 1.5–1.6 M ammonium sulfate, 10% dioxane, and 0.1 M MES (pH 6.5). 1 μl of the crystallization solution was added to 1 μl of the protein solution at concentration 6–8 mg/ml (approximately 0.1 mM) in buffer A. Approximately 0.3 μl of a 40 mM zwittergent 3-12 stock solution was added directly to the hanging drop as an additive. Crystals of Ad2pb grew over 4–8 weeks at 15°C, reaching dimensions of 100 × 75 × 30 μm3. Prior to flash freezing, crystals were soaked for 5 min in 20% sucrose, 1.8 M ammonium sulfate, 10% dioxane, and 0.1 M MES (pH 6.5) as a stabilizing and cryoprotecting solution.
Reference: 15629723 |
Human Adenovirus 2 Penton Base In Complex With An Ad2 N-Terminal Fibre Peptide
(1x9t) |
For the crystallization of the Ad2 penton base/fiber peptide complex, a 3-fold molar excess of peptide was added to the Ad2pb protein and incubated on ice for 30 min prior to addition of crystallization buffer and zwittergent 3-12. The average crystal size was 75 × 75 × 10 μm3 for the Ad2pb fiber peptide complex. (see also xtal conditions for 1x9p)
Reference: 15629723 |
Human Hepatitis B Viral Capsid
(1qgt) |
T=3 and T=4 capsids were crystallized by the vapor diffusion method. Crystals of T=4 capsids were grown from 100 mM NaHCO3 pH 9.5, 100 mM NaCl, 250-350 mM KCl, 9.0-9.5% polyethylene glycol monomethyl ether 5000 (PEG-MME) and 10% 2-propanol diluted 1:1 with freshly prepared capsids (10 mg/ml in 50 mM HEPES pH 7.5, 100 mM KCl). Crystals grew to maximum dimensions of 0.7 x 0.4 x 0.3 mm. Crystals of T=3 capsids grew in 2 weeks from 100 mM NaHCO3 pH 9.5, 100 mM NaCl, 250 mM LiCl, 8-8.5% PEG-MME, 10% 2-propanol. Crystals of T=3 capsids diffracted to aprrox. 8 Å; crystals of T=4 diffracted to 4 Å resolution.
Reference: 10394365 |
Human Papilloma Virus 16 L1 Capsid
(1dzl) |
Deletion mutant of HPV16 L1 lacking in the N-terminal 10 residues yielded good crystals in the presence of 7.5% PEG in 0.2 M NaOAc buffer (pH 4.5). Among the several crystal forms obtained, the space group of the form used in the structure determination was P213
Reference: 10882140 |
Human Rhinovirus 14 Mutant C199Y
(1rmu) |
Cubic mutant HRV14 crystals of the size 0.25 to 0.45 mm were obtained by hanging drop vapor diffusion technique as described for HRV14 by Arnold et al. (1984) J.Mol.Biol. 177, 417-430: The crystals were grown at room temperature. The starting virus concentration in a drop was 0.5 mg/ml with 0.125% (w/v) or 0.25% (w/v) PEG 8000, 0.01 M CaCl2 in 0.01 M Tris.HCl (pH 7.2). The initial concentration of precipitants in the reservoir was 0.25% (w/v) or 0.5% (w/v) PEG 8000 respectively, 0.02 M CaCl2 in 0.01 M Tris.HCl (pH 7.2). Some of the crystals used in collecting the native data sets were also grown in the presence of 0.01 M dithiothreitol. Calcium ions were included as a measure to improve virus stability.
Reference: 2544734 |
Human Rhinovirus 14 Mutant I2170V/Win54954 Complex
(2hwc) |
No information available
Reference: 8383771 |
Human Rhinovirus 14 Mutant I2170V/Win65291 Complex
(2hwb) |
No information available
Reference: 8383771 |
Human Rhinovirus 14 Mutant N1105S/Win52035 Complex
(1ruc) |
No information available
Reference: 7473717 |
Human Rhinovirus 14 Mutant N1105S/Win52035 Complex
(1rud) |
No information available
Reference: 7473717 |
Human Rhinovirus 14 Mutant N1219A
(1ruf) |
No information available
Reference: 7473717 |
Human Rhinovirus 14 Mutant N1219A/Win52035 Complex
(1rue) |
No information available
Reference: 7473717 |
Human Rhinovirus 14 Mutant N1219S/Win52035 Complex
(1rug) |
No information available
Reference: 7473717 |
Human Rhinovirus 14 Mutant N1219S/Win52084 Complex
(1ruh) |
No information available
Reference: 7473717 |
Human Rhinovirus 14 Mutant S1223G
(1ruj) |
No information available
Reference: 8383239 |
Human Rhinovirus 14 Mutant V188L
(2rmu) |
Same as for PDB ID:1rmu
Reference: 2544734 |
Human Rhinovirus 14/Fab Complex
(1rvf) |
The complex was crystallized using the vapour diffusion method, with a reservoir containing 1 ml of 10 mM Tris buffer, pH 7.5, 250-300 mM NaCl, 10 mM CaCl2, and 0.75% PEG 8000. Each sitting drop contained 20 ul of the complex to which 20 ul of precipitating buffer (10mM Tris buffer, pH 7.5, 10 mM CaCl2, and 0.75% PEG 8000) was added. Crystals with a cubic habit usually appeared in 10-14 days and grew up to 0.8 mm in width within one month.
Reference: 8848050 |
Human Rhinovirus 14/Pleconaril Complex
(1na1) |
No information available |
Human Rhinovirus 14/Pleconaril Complex
(1ncq) |
No information available |
Human Rhinovirus 14/Sch38057 Complex
(1hri) |
No information available |
Human Rhinovirus 14/SDZ 35-682 Complex
(1hrv) |
No information available |
Human Rhinovirus 14/WinI(R) Complex
(2rr1) |
No information available |
Human Rhinovirus 14/WinI(S) Complex
(2rs1) |
No information available |
Human Rhinovirus 14/WinII(SR) Complex
(2rm2) |
No information available |
Human Rhinovirus 14/WinIII(S) Complex
(2rs3) |
No information available |
Human Rhinovirus 14/WinIV Complex
(2r04) |
No information available
Reference: 2558377 |
Human Rhinovirus 14/WinR61837 Complex
(1r09) |
R 61837 was dissolved in DMSO to a concentration of 1 to 1.6 mg/ml, and then diluted 5-fold in a buffer of 10 mM-Tris (pH 7.2) containing 2% (w/v) polyethylene glycol 8000. A portion (250 ul) of this solution was added to an equal volume of the same buffer containing HRV14 crystals (space group P2(1)3 with a=445.1Å) to achieve a final R 61837 concentration of 100 to 160 ug/ml. Crystals of HRV14 were soaked in this solution for 7 to 11 days.
Reference: 1847215 |
Human Rhinovirus 14/WinV(S) Complex
(2rs5) |
No information available |
Human Rhinovirus 14/WinVI Complex
(2r06) |
No information available
Reference: 2558377 |
Human Rhinovirus 14/WinVII Complex
(2r07) |
No information available
Reference: 2558377 |
Human Rhinovirus 14/WinVIII Complex
(1r08) |
No information available
Reference: 2558377 |
Human Rhinovirus 16
(1nd2) |
No information available |
Human Rhinovirus 16
(1aym) |
The hanging drop vapor diffusion method was employed in the crystallization of HRV 16. The resevoir solution (0.5 ml in volume) contained PEG 8000 (0.5-1.5%) in buffer. A 5 µl drop of virus solution, concentrated to 8-10 mg/ml, was diluted with 5 µl of reservoir solution. The drop was placed on a plastic coverslip which was used to seal the well. Conditions for crytsallization varied with respect to CaCl2 concentration present in the well solution (5-20 mM). A key factor in the crystallization of HRV 16 was the use of NaCl in the buffer.
Reference: 9083115 |
Human Rhinovirus 16
(1ayn) |
The hanging drop vapor diffusion method was employed in the crystallization of HRV16. The reservoir solution (0.5 ml in vol ume) contained PEG 8000 (0.5~1.5 %) in buffer. A 5 ul drop of virus solution, concentrated to 8-10 mg ml-1, was diluted with 5 ul of reservoir solution. The drop was placed on a plastic coverslip which was used to seal the well. Conditions for crystallization varied with respect to CaCl2 concentration present in the well solution (5-20 mM). A key factor in the crystallization of HRV16 was the use of NaCl in the buffer. The antiviral agent WIN 56291 was soaked into grown crystals.
Reference: 7915182 |
Human Rhinovirus 16/Antiviral C Complex
(1qju) |
The virus was crystallized by using the hanging drop method. Viral particles at a concentration of 8-10 mg/ml in 0.25 mM Hepes, pH 7.5 were mixed with an equal volume of reservoir solution, 0.5-1.5% PEG 8000. Crystals were typically 0.2 mm × 0.2 mm × 0.2 mm. The antiviral compounds were provided by the former Sterling-Winthrop company and soaked into the crystals as described by Smith et al. (Science (1986) 233, 1286-1293) using a concentration of about 100 µg/ml in 0.2% DMSO.
Reference: 10611281 |
Human Rhinovirus 16/Antiviral C Complex
(1qjx) |
Same conditions as described for 1qju
Reference: 10611281 |
Human Rhinovirus 16/Antiviral C Complex
(1qjy) |
Same conditions as described for 1qju
Reference: 10611281 |
Human Rhinovirus 16/HIV Type 1 V3 Loop Chimera
(1k5m) |
Crystals of the MN-III-2 chimera were grown at room temperature using the hanging-drop vapor diffusion method. The crystallization solution consisted of 1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5. A broad-spectrum antiviral agent, SDZ 880061 [72], was dissolved in DMSO and diluted to 0.12 M and mixed with the virus sample (5 mg/ml in 10 mM Tris-HCl, 0.1 M NaCl, pH 7.2) at a volume ratio of 1:20 corresponding to a molar ratio of 10:1. Hanging drops were created by mixing 3–5 μl of this virus solution with an equal volume of the crystallization solution on a plastic coverslip and placing the inverted coverslips over reservoirs containing 1 ml of crystallization solution. Plate-shaped crystals began to appear after 1–2 days and grew to approximately 0.1 × 0.4 × 0.4 mm within a week.
Reference: 12121655 |
Human Rhinovirus 16/Pleconaril Complex
(1ncr) |
No information available |
Human Rhinovirus 16/Pleconaril Complex
(1c8m) |
No information available |
Human Rhinovirus 16/Pleconaril Complex
(1nd3) |
No information available |
Human Rhinovirus 1A/R61837 Complex
(2hwf) |
No information available
Reference: 8383771 |
Human Rhinovirus 1A/Win54954 Complex
(2hwe) |
No information available
Reference: 8383771 |
Human Rhinovirus 1A/Win56291 Complex
(2hwd) |
No information available
Reference: 8383771 |
Human Rhinovirus 2
(1fpn) |
HRV Serotype 2 crystallized in three different morphologies using the hanging drop vapor diffusion method. Typically 2-5 µl of virus solution (5 mg/ml) in 50 mM TRIS-HCl (pH 7.4) was mixed with an equal or smaller volume of reservoir solution. The cyrstals with prismatic morphology and dimensions up to 0.3 x 0.2 x 0.15 mm diffracted to high resolution (beyond 1.8 Å). The crystals were grown at room temperature and pH 7.5 using 0.4 M ammonium sulfate and 0.1 M sodium/potassium phosphate.
Reference: 10903863 |
Human Rhinovirus 2/Receptor Fragment Complex
(1v9u) |
Purified HRV2 and V23 were incubated overnight at 4 °C at a molar ratio of 1:120 to form the complex before the crystallization experiments. Orthorhombic crystals belonging to space group P21221 (a = 308.7 Å, b = 352.2 Å, c = 380.5 Å) were obtained at room temperature by vapor diffusion in hanging drops of 3 ul of the complex solution (2 mg ml-1 in 50 mM Tris-HCl, pH 7.4) with an equal or smaller volume of a reservoir solution containing 0.6 M ammonium sulfate and 0.1 M sodium-potassium phosphate at pH 7.0. Crystals were cryoprotected by soaking for 1 min in a solution containing 30% (v/v) glycerol in the crystallization buffer.
Reference: 15064754 |
Human Rhinovirus 3
(1rhi) |
The hanging drop method was used to crystallize HRV Serotype 3. The reservoir solution contained 10 mM CaCl2 and 0.75% PEG 8000 in a 0.25 M HEPES/0.75 M NaCl/pH 7.2 buffer. The hanging drop contained 5 µl of 10 mg/ml virus mixed with 5 µl of reservoir solution.
Reference: 8939746 |
Human Rhinovirus Mutant S1223G/Win52084 Complex
(1rui) |
No information available
Reference: 7473717 |
Human Rhinovirus Serotype 14
(4rhv) |
Crystals were grown at room temperature in vapor diffusion cells that were coated with Dow Corning 4 compound to reduce nucleation and to prevent crystals from adhering to the glass surface of the wells. A solution of ammonium sulfate (x% saturated) containing 100 mM sodium phosphate buffer at pH 7.2 and 1 mM sodium azide was added to an equal volume of a solution containing R14 virus at y mg/ml (in which 2 < y < 20 mg/ml) such that the product xy was numerically between 5 and 10 units. The solution was put into a well of the diffusion chamber and equilibrated against ammonium sulfate at around 2.5% saturation. Crystals then grew up to 0.6 mm in length within a few days to a week.
Reference: 2856083 |
Human Rhinovirus Serotype 1A
(1r1a) |
50 µl of 3 to 5 mg virus/ml was placed into micro-dialysis button, sealed with membrane and dialyzed at 6 ° C against 0.15 M ammonium formate adjusted to pH 7.35. Long hexagonal shaped crystals were obtained within 2 weeks.
Reference: 2555523 |
Human Rhinovirus/SDZ 880-061 Complex
(1vrh) |
No information available
Reference: 8648640 |
Immature Dengue-2 Prm Virus
(1n6g) |
No information available |
L-A Virus
(1m1c) |
Crystals were obtained in the presence of 10% ethylene glycol, 3% PEG 8000, 1.0 M LiCl, 0.1 M Hepes, pH 7.0 and 10 mg/ml L-A virus.
Reference: 11562160 |
Mengo Encephalomyocarditis Virus
(2mev) |
An orthorhombic crystals were prepared by hanging drop vapor diffusion method with 2.8% PEG 8000 in 0.1 M phosphate buffer at pH 7.4 in the reservoir with an initial virus concentration of 5 mg/ml and 1.4% PEG 8000 in the same buffer in the hanging drop. The crystals grew in 1-2 days at room temperature to a maximum dimension of 0.8 mm. |
Mengo Encephalomyocarditis Virus (pH 4.6)
(1mec) |
No information available |
Mice Minute Virus (MVM), Strain I
(1mvm) |
Crystals were grown using hanging drop vapor diffusion method with conditions similar to those used for CPV. The reservoir solution contained 0.75% (W/V) PEG 8000 and 8 mM CaCl2.2H2O in 10 mM hanging drop produced by mixing 5 ml of virus solution (10 mg/ml) in 10 mM TRIS-HCl at pH 7.5 with 5 µl of reservoir solution. Crystals grew to a maximum dimension of 0.4 mm in about 4 to 8 weeks. |
Murine Polyoma Virus
(1sie) |
For complex formation, the crystals (of Murine Polyoma virus - 1sid) were soaked in harvest buffer also containing 20mM oligosaccharide for 24 h prior to data collection.
Reference: 8805524 |
Murine Polyoma Virus
(1sid) |
Crystals were grown from sodium sulfate using hanging drop method and salanized coverslips. The 2 µl drops contained 6-8 mg/ml virus, 10 mM HEPES pH 7.5, 0.25-0.3 M sodium sulfate and 2.5-5.0% (V/V) glycerol; the reservoir contained 0.55-0.6 M soidium sulfate, 10 mM HEPES pH 7.5 and 5-10% glycerol. Harvest buffer contained 0.65 M sodium sulfate, 50 mM HEPES pH 7.5 and 10% glycerol. For oligosaccharide complex formation, the crystals were soaked in harvest buffer 24 h prior to data collection.
Reference: 8805524 |
Nudaurelia Capensis ω Virus
(1ohf) |
NwV was crystallized using the sitting-drop method of vapor diffusion (McPherson, 1982). The reservoir solution was prepared using 0.075M morpholinopropanesulfonic acid (MOPS) buffer at pH 7-0 with polyethylene glycol (PEG) 8000 at 2%, CaCI2 at 0.25 M and NaN3 at 10 -3 M. The virus solution was at 8-10 mg ml -1 in 0.07M sodium acetate buffer at pH 5.0. The crystallization drops consisted of 10 ul of the virus solution mixed with 40 ul of the reservoir solution. This mixture was allowed to reach vapor equilibrium with the reservoir solution (20 ml). Tabular shaped crystals appeared in 2-4 weeks.
Reference: 14972547 |
Pariacoto Virus (PAV)
(1f8v) |
PaV was crystallized by the hanging drop vapor diffusion method at room temperature. The reservoir was 1ml of 75 mM Li2SO4, 5mM CaCl2, and 4% (W/V) PEG 8000 in 50 mM Tris-HCl buffer, pH 7.5. The droplet was a mixture of 1 µl reservoir solution and 1 µl virus sample at a virus concentration of aprox. 20 mg ml-1 in 50 mM Tris-HCl buffer, pH 7.5. Crystals appeard within 4-5 days.
Reference: 11135676 |
Physalis Mottle Virus
(1e57) |
Crystals of the recombinant capsids were obtained by precipitating capsids at a concentration of 80-100 mg/ml in 0.5 M sodium acetate buffer (pH 5.6), 10 mM dithiothreitol and 2 mM CaCl2 using 2-4 % (w/v) PEG 8000.
Reference: 11286554 |
Physalis Mottle Virus (PhMV)
(1qjz) |
No information available
Reference: 10369772 |
Poliovirus (Mahoney Strain)
(1hxs) |
No information available |
Poliovirus (Type 1, Mahoney Strain)
(1asj) |
No information available
Reference: 9253417 |
Poliovirus (Type 1, Mahoney Strain) Mutant H2142Y
(1ar9) |
No information available |
Poliovirus (Type 1, Mahoney Strain) Mutant P1095S
(1ar8) |
No information available |
Poliovirus (Type 1, Mahoney Strain) Mutant P1095S, H2142Y
(1ar7) |
No information available |
Poliovirus (Type 1, Mahoney Strain) Mutant V1160I
(1al2) |
No information available |
Poliovirus (Type 1, Mahoney Strain) Mutant V1160I, P1095S
(1ar6) |
No information available |
Poliovirus (Type 1, Mahoney Strain)/R77975 Complex
(1po2) |
The crystallization procedure is same as given for virus-drug R80633. Because crystals were damaged by direct transfer to saturated solutions of R77975, crystals were first equilibrated with a 50% saturated solution for a few days before transfer to the higher concentration.
Reference: 15299887 |
Poliovirus (Type 1, Mahoney Strain)/R78206 Complex
(1vbd) |
Crystals of native virus were soaked in freshly prepared saturated solutions of drug at 4°C for 1–2 weeks.
Reference: 7820548 |
Poliovirus (Type 1, Mahoney Strain)/R80633 Complex
(1po1) |
(The virus was) crystallized by microdialysis versus low ionic strength. Prior to use, crystals grown in dialysis buttons were equilibrated versus a synthetic mother liquor containing 25%(v/v) ethylene glycol in PMC7 buffer (10 mM NaPIPES, 5 mM MgCI2, 1 mM CaCI2, pH 7.0). Solid drug was dissolved in dimethyl sulfoxide (DMSO) at 10mg m1-1 and stored at 193 K until use. Freshly grown crystals of the native virus were soaked in freshly prepared saturated solutions of drug at 277 K for at least a week.
Reference: 15299887 |
Poliovirus (Type 3, Sabin Strain) Mutant F124L, F134L/R78206 Complex
(1vbe) |
Crystals of native virus were soaked in freshly prepared saturated solutions of drug at 4°C for 1–2 weeks.
Reference: 7820548 |
Poliovirus (Type 3, Sabin Strain)/R78206 Complex
(1vba) |
Crystals of native virus (P3/Sabin - Pilman et al., EMBO J 8 (1989), pp. 1567–1579) were soaked in freshly prepared saturated solutions of drug at 4°C for 1–2 weeks. The 1-week soaking time required for maximal occupancy of R78206 in P3/Sabin had previously been determined by comparing symmetry-averaged difference Fourier maps calculated from incomplete (3–4 film) data sets obtained from crystals soaked for various lengths of time.
Reference: 7820548 |
Poliovirus (Type 3, Sabin Strain)/Win51711 Complex
(1piv) |
The purified virus (P3/Sabin) was crystallized by microdialysis versus progressively lower concentrations of NaC1 in PMC7 buffer (10 mM PIPES, 5 mM MgC12, 1 mM CaCI2, pH 7.0) at 277K. Crystals generally began to appear at approximately 0.6M NaCI and crystal growth was complete in one to two months. The solid drug (WIN51711) was dissolved at a concentration of approximately 10 mg/m1 in neat dimethyl sulfoxide and this stock solution was stored at 193K until use. (Fresh grown virus) crystals were transferred into the saturated drug solution, soaked for two weeks at 277 K, and mounted in sealed quartz capillary tubes for data collection.
Reference: 15299834 |
Poliovirus (Type3, Sabin Strain)/R77975 Complex
(1vbc) |
Crystals of native virus were soaked in freshly prepared saturated solutions of drug at 4°C for 1–2 weeks.
Reference: 7820548 |
Poliovirus (Type3, Sabin Strain)/R80633 Complex
(1vbb) |
Crystals of native virus were soaked in freshly prepared saturated solutions of drug at 4°C for 1–2 weeks.
Reference: 7820548 |
Poliovirus Type 1 (Mahoney Strain)
(2plv) |
No information available
Reference: 2548847 |
Poliovirus Type 1 (Mahoney Strain) Empty Capsid
(1pov) |
Crystals of empty capsids were grown by dialyzing 5-15 µl samples of empty capsid (approx. 15 mg/ml) initially in 0.8 M NaCl, PMC7 ( 10 mM PIPES, 5 mM MgCl2 at 4 ° C.
Reference: 2994218 |
Poliovirus Type 3 (Sabin Strain)
(1pvc) |
No information available |
Poliovirus Type2/Sch48973 Complex
(1eah) |
Crystals were grown at room temperature using a modified version of the hanging drop vapor diffusion method. The reservoir solution (0.5 ml total volume) contained varying amounts of PEG 8000 (0.9-1.4%) and lithium sulfate (100-250 mM). The virus sample, 2-3 µl of a 5 mg/ml solution, was placed on a plastic coverslip and mixed with an equal volume of the reservoir solution. The well was sealed with the coverslip using vacuum grease except for a small leak that was left between the coverslip and the well. After2-4 days, crystals approx. 0.1mm x 0.2mm x 0.1 mm began to appear, at which time the leak was sealed with vacuum grease and the crystals were allowed to grow to their maximum size of 0.2 mm x 0.35 mm x 0.2 mm. Without the leak, the crystallization drops would either form precipitate or remain clear for months. The leak left between coverslip and the well was a key factor in the production of crystals suitable for X-ray diffraction analysis.
Reference: 9261087 |
Porcine Parvovirus
(1k3v) |
Crystals were grown at 18°C in 20 mM Hepes-NaOH (pH 6.5), containing 8 mM CaCl, 0.05% (w/v) sodium azide and with 1.0% or 1.5% PEG 8000 as a precipitant. The crystals grew as thin plates over a period of several weeks to a maximum size of approximately 0.2 mm x 0.02 mm x 0.01 mm.
Reference: 11827486 |
Recombinant T=3 capsid of a site specific mutant of SeMV CP
(1x35) |
The best crystals of rCP were obtained using the hanging-drop method when the capsid at a concentration of 10 mg ml-1 was precipitated with 4% PEG 3350, 0.1 M MgCl2, 5% isopropanol and 0.05 M HEPES pH 7.5. For CP-P53A, a combination of 10-12%(w/v) PEG 3350 with 0.1-0.3 M Li2SO4, 5% isopropanol and 0.05 M HEPES pH 7.5 gave good crystals. The capsids crystallized in space group R3 for rCP and C2 for CP-P53A (PDB ID: 1x33). The unit cells of rCP and CP-P53A are compatible with one and two VLPs, respectively.
Reference: 16204893 |
Red Clover Mottle Virus
(rcmv) |
Elongated RCMV crystals were produced by the sitting drop vapor diffusion method. The starting solution contained 10 mg of RCMV per ml in 10 mM sodium phosphate (pH 7). The reservoir solution contained 50 mM potassium phosphate (pH 7), 1.8% polyethylene glycol 8000, 0.3 M ammonium sulfate, 2 mM EDTA, and 1 mM sodium azide. Equal volumes of the virus and reservoir solution were mixed and equilibrated with the reservoir solution at room temperature. The crystals grew to 0.5 to 1 mm in all dimensions after 5 to 7 days.
Reference: 10590139 |
Reovirus Core
(1ej6) |
For crystallization, Reovirus cores (6 mg/ml in 0.5 M NaCl, 0-0.3 M NaOAc, 50 mM MgCl2, 50 mM Hepes, pH 7) were equilibrated against 1 M NaCl, 0-0.6 M NaOAc, 100 mM HEPES, pH 7.0. Crystals, 150-200 µm at their largest dimensions, grew in 9-12 months. They were transferred to a solution containing 0.8 M NaOAc (but otherwise identical to the well solution) and mounted in capillaries.
Reference: 10801118 |
Rice Dwarf Virus
(1uf2) |
Purified virus was crystallized with the vapor diffusion method using PEG 8000 as a precipitant at 4 °C and 20 °C. The reservoir solution contained 0.1 M-histidine, 0.01 M-MgCl2, 0.1 to 4.0% (w/v) PEG 8000, and was adjusted to pH 6.0. Crystals were obtained in as little as 12h from the high concentration of precipitant solution to 20 °C, although the crystal size was less than 0.1 mm in diameter. The optimal crystallization conditions were that the hanging drop contained a mixture of 6 ul of 1 mg RDV/ml and 3 ul of reservoir solution. The reservoir wells were filled with 800 ul of 0.4 to 0.5% PEG 8000 solution.
Reference: 2056533 |
Rice Yellow Mottle Virus
(1f2n) |
The crystallization was carried out by vapor diffusion and the reservoir solution was 50 mM sodium citrate, pH 3.0, 200 mM lithium sulfate, and 3.6% (W/V) PEG 8000. The virus solution was concentrated to 36 mg/ml.
Reference: 11080631 |
Satellite Panicum Mosaic Virus
(1stm) |
Cubic crystals grown by vapor diffusion methods using glass depression plates in plastic sandwich boxes at 4 ° C over a period of about one month. The reservoir solution was 37% saturated ammonium sulfate in water. The droplets were composed of 10 µl of a 10 mg/ml virus solution (buffered with 20 mM potassium phosphate) plus 10 µl of the reservoir.
Reference: 8182753 |
Satellite Tobacco Mosaic Virus
(1a34) |
Protein was four times recrystallized from bulk solution by addition AF ammonium sulfate to 15% saturation. Space crystals were grown by liquid-liquid diffusion in a microgravity environment over 12 days aboard IML-I mission of the US space shuttle.
Reference: 2585487 |
Satellite Tobacco Necrosis Virus
(2stv) |
Crystals grown from solutions containing 10-12 g of virus/l (or 7-8 g of virus/l and 0.4% (W/V) PEG 6000) in 1mM Mg(2+), 50mM sodium phosphate pH 6.5.
Reference: 3681993 |
Satellite Tobacco Necrosis Virus
(2buk) |
No information available
Reference: 6481804 |
Sesbania Mosaic Virus (SMV)
(1smv) |
The purified virus was crystallized by vapor diffusion in depression slides. Best crystals were obtained by precipitating the virus (30 mg/ml in 0.1 M sodium acetate (pH 5.6)) with 15% to 20% saturated ammonium sulfate in the inner well and 30% saturated in the outer well. Addition of divalent salts had pronounced effect on crystal growth.
Reference: 8421301 |
Sesbania Mosaic Virus Deletion Mutant Cp-N(δ)36
(1vb4) |
See xtal conditions for 1vak
Reference: 1534225 |
Sesbania Mosaic Virus Deletion Mutant Cp-N(δ)65
(1vak) |
Crystals of these CP mutant capsids were obtained by precipitating capsids at a concentration of 10–15 mg/ml in 0.1 M Hepes buffer (pH 7.5), 0.1% (v/v) isopropanol and 0.2 M MgCl2 using 4–6% (w/v) PEG 3350. While CP-NΔ36 and CP-NΔ65 crystallized in space group P2(1), CP-NΔ65-D146N-D149N crystallized in space group P1 with a full virus-like particle in the crystallographic asymmetric unit.
Reference: 1534225 |
Sesbania Mosaic Virus Deletion Mutant Cp-N(δ)65-D146N-D149N
(1vb2) |
See xtal conditions for 1vak
Reference: 1534225 |
Simian Virus 40
(1sva) |
Crystals were grown at 25 ° C (by hanging drop technique) from a solution containing approx. half-saturated ammonium sulfate buffered with either TRIS(hydroxymethyl)aminomethane or ammonia to pH 7.0 to 7.5, 10 mM Mg(2+) and 0.5 mM Ca(2+). The concentration of virus was 5 to 10 mg/ml. Morphologically the crystals were cubes.
Reference: 8805523 |
Southern Bean Mosaic Virus (SBMV)
(4sbv) |
The virus was crystallized in vials from 0.95 M ammonium sulfate with an initial virus concentration of 20 mg/ml.
Reference: 3681993 |
Swine Vesicular Disease Virus
(1oop) |
SVDV (strain UKG/27/72) was purified by sucrose density gradient centrifugation, and the resultant material (at a concentration of 10 mg/ml) was crystallized by the sitting-drop vapor diffusion method by mixing equal volumes with the reservoir solution containing 15 to 25% saturated ammonium sulfate in 100 mM phosphate buffer (pH 7.6). The "toblerone" morphology crystals were of dimensions 0.1x0.0.1x0.2 mm3
Reference: 12692248 |
Swine Vesicular Disease Virus
(1mqt) |
SVDV was crystallized in three different crystal morphologies (space groups C2, P2(1)2(1)2(1) and I222) using the hanging drop vapour diffusion method. Typically, 2ul of virus solution (5 - 10 mg ml -1) in water were mixed with an equal volume of a reservoir solution. Crystals belonging to space group I222 were obtained at room temperature and pH 6.2 using 1.2M ammonium sulfate and 0.1M sodium/potassium phosphate.
Reference: 12595720 |
T=1 capsid of an amino-terminal deletion mutant of SeMV CP
(1x36) |
The purified CP-N31 capsids were used for crystallization at a concentration of 6 mg/ml using the hanging-drop vapour-diffusion method. Good crystals were obtained in 0.1 M HEPES buffer pH 7.5 containing 6%(w/v) PEG 3350, 0.2 M MgCl2 and 0.1%(v/v) isopropanol. The crystals belonged to space group P212121 and contained a full VLP in the asymmetric unit.
Reference: 16204894 |
T=1 Particle of Brome Mosaic Virus
(1yc6) |
Polyhedral crystals of the T=1 BMV particles as large as 0.5 mm on edge were grown for X-ray diffraction analysis using conventional procedures. These utilized vapor diffusion in Cryschem sitting drop plates using drop volumes of 6–10 μl. Optimal conditions were identified, and these were droplets composed of equal volumes of the particle solution and 2.1 M sodium malonate at pH 7.5. Reservoirs of 0.65 ml of the 2.1 M malonate were equilibrated with the microdrops at room temperature for approximately two to four weeks before crystals were harvested.
Reference: 15713465 |
Theiler's Murine Encephalomyelitis Virus (BeAn Strain)
(1tmf) |
Crystals grown by hanging drop vapor diffusion method with PEG 3350 in 0.02 M boric acid buffer (pH 8.5).
Reference: 1312722 |
Theiler's Murine Encephalomyelitis Virus (DA Strain)
(1tme) |
Concentrated samples of virus (10 mg/ml) were crystallized at 4 ° C by microdialysis verses progressively lower concentrations of NaCl in 10 mM Na PIPES buffer (pH 7.0-7.3).
Reference: 1549565 |
Tobacco Necrosis Virus (TNV)
(1tnv) |
No information available
Reference: 15299356 |
Tobacco Necrosis Virus (TNV)
(1c8n) |
Crystals grown by dialysis method using microdialysis cells by both lowering pH and increasing salt concentration. Virus solution was dialyzed against 0.4 M sodium phosphate buffer with the pH adjusted to 6.0. Sometimes thin plate like crystals were produced with the dodecahedral crystals in the same dialysis cells. the thin plate like crystals were dissolved by dialyzing against 10 mM sodium phosphate buffer (pH 7.0). When the cells were transferred to the crystallization buffer, dodecahedral crystals were usually produced.
Reference: 10864506 |
Tobacco Ringspot Virus
(1a6c) |
Virus was crystallized using hanging drop setting from reservoir buffer containing 2-3% (W/V) PEG 3350, 1mM sodium azide and 0.125 M potassium phosphate, pH 6.5
Reference: 9519407 |
Tomato Bushy Stunt Virus (TBSV)
(2tbv) |
The virus was crystallized by adding saturated ammonium sulfate to the virus (approx. 30 mg/ml in water) until the solution just remained turbid. The final concentration of ammonium sulfate at this endpoint was approx. 0.5 M but varied from preparation to preparation. The solution was distributed into stoppered vials and stored at 4 ° C. At this temperature the turbidity vanished and single crystals grew after a period of weeks or months. Seeding accelerated the process, but several months were necessary to obtain large crystals (0.3 to 0.5 mm).
Reference: 1177320 |
Tomoto Aspermy Virus
(1laj) |
Crystals were grown by vapor diffusion using sitting drops in Cryschem plates (Hampton Research, Laguna Niguel, CA) sealed with clear plastic tape. Drops contained 10 µl of virus suspension mixed with 10 µl of precipitant in vapor equilibrium with 1 ml of precipitant in the reservoir. Crystals grew to full size in about 2 weeks.
Reference: 12406691 |
Turnip Yellow Mosaic Virus (Artificial Top Component)
(1w39) |
Crystals of Artificial Top Component (ATC of TYMV) were grown in 1.16–1.22 M ammonium phosphate (pH 4.5) at room temperature, using the sitting-drop, vapor-diffusion method. A large number of small crystals appeared within a few days from mixing 5 μl of protein solution with an equal volume of precipitant solution. Crystals of ATC with the RNA hairpin were obtained by crystallization with a protein to ligand molar ratio of 1:50. MgCl2 (10 mM) was added to the precipitant solution to replace the spermidine, which is naturally present in TYMV. Spermidine is subject to oxidation and therefore not suitable for this type of experiment. Furthermore, RNase inhibitor (RNA Guard, Pharmacia) was added in a 1:50 (v/v) dilution to the crystallization droplet to prevent the RNA oligonucleotide from degradation. Mixing equal volumes of protein solution, in the presence of 50 equivalents of RNA hairpin, with reservoir solution, again resulted in a large amount of rather small crystals, which were not suitable for X-ray crystallography. In order to grow larger crystals, the protein concentration was lowered to 10 mg ml−1 and 5 μl of this protein solution was mixed with an equal volume of precipitant solution. After equilibration, macroseeds obtained from previous crystallization trials were washed in reservoir solution and transferred to the new crystallization droplets. In these drops, no spontaneous nucleation had occurred and the macroseeds grew into large crystals with dimensions up to 0.6 mm×0.4 mm×0.25 mm.
Reference: 15321716 |
Turnip Yellow Mosaic Virus (TYMV)
(1auy) |
Crystals grown using hanging drop vapor diffusion technique. The reservoir solution contained between 1.09 and 1.17 M ammonium phosphate and 100mM MES buffer with a final pH of 3.7-5.5. 5 µl of virus solution (16 mg/ml) 5 µl of reservoir solution composed of the micro-drops yeilded large crystals at 25 ° C.
Reference: 7716173 |
