7KOM
High Resolution Crystal Structure of Putative Pterin Binding Protein PruR (VV2_1280) from Vibrio vulnificus CMCP6
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 3.5 | 292 | Protein: 7.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (A7), 0.1M Citric acid (pH 3.5), 3.0M Sodium chloride. Cryo: 4.0M Formate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.046 | α = 90 |
b = 71.087 | β = 90 |
c = 106.359 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | MARMOSAIC 300 mm CCD | Be | 2018-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 0.99 | 30 | 93.4 | 0.075 | 0.075 | 0.081 | 0.03 | 45.1 | 7.3 | 65367 | -3 | 6.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 0.99 | 1.01 | 82.2 | 0.679 | 0.679 | 0.74 | 0.288 | 0.821 | 3.2 | 6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 0.99 | 26.6 | 62187 | 3176 | 93.21 | 0.1205 | 0.1195 | 0.141 | RANDOM | 9.117 |
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] | |
-1.07 | 0.61 | 0.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.417 |
r_dihedral_angle_4_deg | 13.304 |
r_dihedral_angle_3_deg | 9.826 |
r_rigid_bond_restr | 9.196 |
r_dihedral_angle_1_deg | 4.926 |
r_angle_refined_deg | 1.53 |
r_angle_other_deg | 1.389 |
r_chiral_restr | 0.084 |
r_gen_planes_refined | 0.008 |
r_bond_refined_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1098 |
Nucleic Acid Atoms | |
Solvent Atoms | 254 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |