2Z9D
The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1V4B | PDB ID 1V4B |
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.93 | 57.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.065 | α = 90 |
b = 89.892 | β = 90 |
c = 101.872 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | CCD | ADSC QUANTUM 210 | 2003-11-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0000 | Photon Factory | AR-NW12A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 67.42 | 29939 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ID 1V4B | 2.1 | 41.17 | 28382 | 1519 | 99.03 | 0.17202 | 0.16979 | 0.21395 | RANDOM | 23.502 |
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] | |
2.57 | -1.51 | -1.06 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.739 |
r_dihedral_angle_4_deg | 21.554 |
r_dihedral_angle_3_deg | 12.641 |
r_dihedral_angle_1_deg | 5.287 |
r_scangle_it | 3.431 |
r_scbond_it | 2.565 |
r_angle_refined_deg | 1.438 |
r_mcangle_it | 1.388 |
r_mcbond_it | 1.182 |
r_angle_other_deg | 0.918 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3040 |
Nucleic Acid Atoms | |
Solvent Atoms | 164 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |