4HCQ
Crystal structure of GLMU from mycobacterium tuberculosis in complex with glucosamine-1-phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3DJ4 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
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 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.19 | 61.43 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 79.27 | α = 90 |
b = 79.27 | β = 90 |
c = 276.73 | γ = 120 |
Symmetry | |
---|---|
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 | 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 | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.6 | 19.932 | 99.4 | 0.088 | 20.1 | 19893 | -3 | 42.49 |
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) | |||||||||||
1 | 2.6 | 2.67 | 94.9 | 0.602 | 2.86 |
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 | 3DJ4 | 2.6 | 19.93 | 19855 | 1011 | 99.5 | 0.202 | 0.199 | 0.265 | RANDOM | 33.01 |
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 | 0.01 | -0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.034 |
r_dihedral_angle_4_deg | 24.951 |
r_dihedral_angle_3_deg | 18.041 |
r_dihedral_angle_1_deg | 7.226 |
r_scangle_it | 4.326 |
r_scbond_it | 2.634 |
r_angle_refined_deg | 1.979 |
r_mcangle_it | 1.73 |
r_mcbond_it | 0.928 |
r_chiral_restr | 0.13 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3309 |
Nucleic Acid Atoms | |
Solvent Atoms | 87 |
Heterogen Atoms | 41 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |