6G58
Structure of the alanine racemase from Staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4A3Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 277 | 0.1 M Sodium acetate pH 4, 10 %(v/v) MPD |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 62.71 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 85.543 | ¦Á = 90 |
b = 106.767 | ¦Â = 90 |
c = 130.835 | ¦Ã = 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 | PIXEL | DECTRIS PILATUS 6M-F | 2015-09-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.979 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.9 | 49.4 | 99 | 0.13 | 1 | 10.7 | 6.7 | 95389 | 28.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.9 | 1.96 | 92 | 0.45 | 1.2 | 6.4 |
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 | 4A3Q | 1.9 | 49.4 | 90599 | 4787 | 99.11 | 0.15224 | 0.15133 | 0.16971 | RANDOM | 34.78 |
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] | |
0.23 | 0.27 | -0.5 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.315 |
r_dihedral_angle_4_deg | 15.48 |
r_dihedral_angle_3_deg | 11.828 |
r_long_range_B_other | 6.809 |
r_long_range_B_refined | 6.808 |
r_dihedral_angle_1_deg | 5.94 |
r_scangle_other | 4.906 |
r_scbond_it | 3.234 |
r_scbond_other | 3.232 |
r_mcangle_other | 2.454 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6020 |
Nucleic Acid Atoms | |
Solvent Atoms | 482 |
Heterogen Atoms | 145 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |
Coot | model building |