3SPT
Crystal structure of GlmU from Mycobacterium tuberculosis in complex with ACETYL COENZYME A and URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DJ4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | sitting drop | 8.5 | 291 | 0.1M Tris-Cl, pH-8.5, 2% Tacsimate, 18% PEG 3350, sitting drop, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.02 | 69.43 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 110.194 | ¦Á = 90 |
b = 110.194 | ¦Â = 90 |
c = 361.295 | ¦Ã = 120 |
Symmetry | |
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Space Group | H 3 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 | MARCCD 225 | mirrors | 2011-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97625 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.33 | 19.808 | 99.8 | 0.054 | 24.88 | 36542 | -3 | 42.057 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.33 | 2.39 | 98.3 | 0.359 | 0.387 | 5.05 |
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 | 3DJ4 | 2.33 | 19.68 | 35443 | 1001 | 99.85 | 0.19291 | 0.19205 | 0.22359 | RANDOM | 31.524 |
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] | |
0.0001 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.4 |
r_dihedral_angle_4_deg | 22.17 |
r_dihedral_angle_3_deg | 17.29 |
r_dihedral_angle_1_deg | 7.186 |
r_scangle_it | 6.09 |
r_scbond_it | 3.798 |
r_angle_refined_deg | 2.353 |
r_mcangle_it | 2.173 |
r_mcbond_it | 1.189 |
r_chiral_restr | 0.246 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3471 |
Nucleic Acid Atoms | |
Solvent Atoms | 212 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |