4G3P
Crystal structure of GlmU from Mycobacterium tuberculosis Snapshot 3
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 | VAPOR DIFFUSION | 7.5 | 277 | 8% PEG 8000, 150MM NACL, 5% GLYCEROL, 1,3-BUTANEDIOL,AMPPNP, MGCL2,0.1M HEPES, COCL2, DTT, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 277K, vapor diffusion |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.05 | 59.73 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 77.47 | ¦Á = 90 |
b = 77.47 | ¦Â = 90 |
c = 277.5 | ¦Ã = 120 |
Symmetry | |
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Space Group | H 3 |
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 | MAR scanner 345 mm plate | MIRRORS | 2009-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.47 | 19.86 | 99.3 | 0.123 | 0.114 | 16.4 | 6.3 | 22217 | 40.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.47 | 2.53 | 92.8 | 0.488 | 0.573 | 3.45 | 5.76 |
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 | 2.47 | 19.86 | 21135 | 1047 | 99.3 | 0.184 | 0.181 | 0.241 | RANDOM | 24.51 |
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] | |
-0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.798 |
r_dihedral_angle_4_deg | 18.874 |
r_dihedral_angle_3_deg | 17.548 |
r_dihedral_angle_1_deg | 7.803 |
r_scangle_it | 4.84 |
r_scbond_it | 2.973 |
r_angle_refined_deg | 2.009 |
r_mcangle_it | 1.805 |
r_mcbond_it | 0.969 |
r_chiral_restr | 0.146 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3374 |
Nucleic Acid Atoms | |
Solvent Atoms | 198 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |