2R70
Crystal structure of infectious bursal disease virus VP1 polymerase, cocrystallized with an oligopeptide mimicking the VP3 C-terminus.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 293 | 5% PEG 3350, 0.4M LiNO3, 0.1M Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.23 | 70.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.801 | α = 90 |
b = 123.801 | β = 90 |
c = 361.843 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2007-08-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.975 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.7 | 107.215 | 95 | 0.1 | 0.1 | 4.9 | 12.2 | 43251 | 43251 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.7 | 2.85 | 96.3 | 0.434 | 0.434 | 1.7 | 12.5 | 6265 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 2.7 | 40 | 43248 | 43248 | 2195 | 93.93 | 0.223 | 0.221 | 0.256 | RANDOM | 48.396 |
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] | |
0.06 | 0.03 | 0.06 | -0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.301 |
r_dihedral_angle_4_deg | 20.276 |
r_dihedral_angle_3_deg | 18.554 |
r_dihedral_angle_1_deg | 5.559 |
r_scangle_it | 2.103 |
r_angle_refined_deg | 1.257 |
r_scbond_it | 1.221 |
r_mcangle_it | 0.997 |
r_mcbond_it | 0.558 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5853 |
Nucleic Acid Atoms | |
Solvent Atoms | 137 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DNA | data collection |
REFMAC | phasing |