3DJ4
Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 8% PEG 8000, 150mM NaCl, 2mM MnCl2, 5% Glycerol, 1,3-butanediol, AMPPNP, MgCl2, DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.6 | α = 90 |
b = 78.6 | β = 90 |
c = 278 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | mirrors | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54179 |
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 | 2.38 | 98.3 | 0.097 | 19.84 | 25334 | -3 | 31.363 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.38 | 2.44 | 82.3 | 0.443 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.38 | 29.03 | 25333 | 1267 | 100 | 0.197 | 0.194 | 0.257 | RANDOM | 24.694 |
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] | |
0.86 | 0.43 | 0.86 | -1.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.116 |
r_dihedral_angle_4_deg | 22.214 |
r_dihedral_angle_3_deg | 15.849 |
r_dihedral_angle_1_deg | 8.467 |
r_scangle_it | 5.457 |
r_scbond_it | 3.574 |
r_angle_refined_deg | 2.544 |
r_mcangle_it | 2.125 |
r_mcbond_it | 1.286 |
r_nbtor_refined | 0.302 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3374 |
Nucleic Acid Atoms | |
Solvent Atoms | 147 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |