7YSM
Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) co-crystallized with UDP-N-acetylglucosamine from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 0.2M Sodium acetate trihydrate, 0.1M Tris pH 8.5 30% PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.69 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 51.114 | ¦Á = 90 |
b = 76.414 | ¦Â = 91.87 |
c = 79.949 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2020-03-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.87 | 50 | 100 | 0.145 | 0.156 | 0.058 | 5.7 | 7.3 | 51063 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.87 | 1.9 | 100 | 0.791 | 0.867 | 0.348 | 0.733 | 5.9 |
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 | 7YS8 | 1.87 | 31 | 48365 | 2677 | 99.73 | 0.1635 | 0.1617 | 0.1954 | RANDOM | 19.547 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.38 | 0.03 | 0.11 | 0.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_bond_refined_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4671 |
Nucleic Acid Atoms | |
Solvent Atoms | 806 |
Heterogen Atoms | 174 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |