4K9Z
Crystal structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus (target NYSGRC-011676), space group P6222
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2LJA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.8 | 298 | Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol); Reservoir (2.0 M Ammonium sulfate; Cryoprotection (20% glycerol), temperature 298K, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.45 | 49.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.96 | α = 90 |
b = 60.96 | β = 90 |
c = 173.89 | γ = 120 |
Symmetry | |
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Space Group | P 62 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 | ADSC QUANTUM 315r | MIRRORS | 2012-10-17 | 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 | 1.8 | 57.963 | 99.9 | 0.076 | 0.076 | 24.5 | 21.3 | 18641 | 18641 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.8 | 1.9 | 100 | 0.721 | 0.721 | 1.1 | 22.3 | 2649 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 | 2LJA | 1.8 | 9.977 | 18454 | 18454 | 945 | 99.97 | 0.2023 | 0.2023 | 0.2001 | 0.2473 | RANDOM | 34.4866 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.836 |
f_angle_d | 1.206 |
f_chiral_restr | 0.078 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1125 |
Nucleic Acid Atoms | |
Solvent Atoms | 90 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
MOSFLM | data reduction |
AMoRE | phasing |