2YI9
Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus in complex with magnesium
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.65 | CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING 200 NL PROTEIN (5.8-6.8 MG/ML) AND 100 NL RESERVOIR SOLUTION (20-18% W/V PEG 3350, 0.10-0.09 M BIS-TRIS PROPANE PH 7.5, 0.2-0.18 M SODIUM CITRATE) EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20.5 DEGREES CELSIUS. CRYSTALS WERE SOAKED BY DILUTING THE MOTHER-LIQUOR WITH APPROX. 0.5 UL 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 8.25 AND 20% V/V GLYCEROL, TRANSFERRING THE CRYSTALS TO A FRESH DROP CONTAINING 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 8.25, 20% V/V GLYCEROL, 50 MM MGCL2 AND 10 UM GTP, AND INCUBATING FOR 10 MIN. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.36 | 63.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 134.048 | α = 90 |
b = 183.874 | β = 90 |
c = 244.521 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2009-06-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.2 | 101.81 | 100 | 0.17 | 10.6 | 7.3 | 304685 | -3 | 28.03 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.26 | 100 | 0.75 | 2.7 | 7.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2PGG | 2.2 | 32.21 | 304439 | 3069 | 100 | 0.1605 | 0.1603 | 0.1812 | RANDOM | 27.7 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.3797 | -1.5091 | 0.1295 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 15.17 |
t_omega_torsion | 3.2 |
t_angle_deg | 0.98 |
t_bond_d | 0.011 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 30143 |
Nucleic Acid Atoms | |
Solvent Atoms | 2989 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |