4KA0
Crystal structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus (target NYSGRC-011676), space group P21221
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol); Reservoir (2000 mM Ammonium sulfate, 100 mM Sodium citrate/ Citric acid pH 5.5; Cryoprotection (20% glycerol), Vapor Diffusion, Sitting Drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.04 | α = 90 |
b = 90.51 | β = 90 |
c = 96.63 | γ = 90 |
Symmetry | |
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Space Group | P 21 2 21 |
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 315r | MIRRORS | 2012-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9793 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.1 | 90.51 | 99.9 | 0.084 | 0.084 | 14.3 | 7.7 | 37055 | 37055 |
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) | ||||||||||
1 | 2.1 | 2.21 | 99.8 | 0.565 | 0.565 | 1.4 | 7.7 | 5318 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2LJA | 2.1 | 42.66 | 37016 | 37016 | 1848 | 99.85 | 0.2083 | 0.2083 | 0.205 | 0.2697 | RANDOM | 39.9103 |
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] | |
2.32 | -2.41 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.444 |
r_dihedral_angle_3_deg | 16.107 |
r_dihedral_angle_4_deg | 13.729 |
r_dihedral_angle_1_deg | 6.389 |
r_mcangle_it | 4.452 |
r_mcbond_it | 3.225 |
r_mcbond_other | 3.224 |
r_angle_refined_deg | 1.714 |
r_angle_other_deg | 0.839 |
r_chiral_restr | 0.099 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4512 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
MOSFLM | data reduction |
AMoRE | phasing |