7KOS
1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein PruR (Atu3496) from Agrobacterium fabrum str. C58
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7KOM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 292 | Protein: 12.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3. Screen: Classics II (C3), 2.4M Sodium malonate pH 7.0 Cryo: 25% Sucrose, 1.2M Sodium malonate pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.462 | α = 90 |
b = 91.81 | β = 90 |
c = 99.22 | 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 | MARMOSAIC 300 mm CCD | Be | 2019-06-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 1.5 | 30 | 99.9 | 0.046 | 0.046 | 0.051 | 0.021 | 31.3 | 5.8 | 118548 | -3 | 21.7 |
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 | 1.5 | 1.53 | 100 | 0.796 | 0.796 | 0.875 | 0.361 | 0.82 | 2.4 | 5.8 |
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 | 7kom | 1.5 | 29.04 | 111854 | 5910 | 99.85 | 0.1525 | 0.1515 | 0.1723 | RANDOM | 25.236 |
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] | |
-0.75 | -0.93 | 1.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.877 |
r_dihedral_angle_4_deg | 14.86 |
r_dihedral_angle_3_deg | 10.249 |
r_dihedral_angle_1_deg | 4.573 |
r_angle_refined_deg | 1.435 |
r_angle_other_deg | 0.402 |
r_chiral_restr | 0.068 |
r_gen_planes_refined | 0.055 |
r_gen_planes_other | 0.051 |
r_bond_refined_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4581 |
Nucleic Acid Atoms | |
Solvent Atoms | 736 |
Heterogen Atoms | 88 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |