5K2X
Crystal structure of M. tuberculosis UspC (tetragonal crystal form)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 292 | 0.12 M of 1,6-Hexanediol; 1-Butanol; 1,2-Propanediol; 2-Propanol; 1,4-Butanediol; 1,3-Propanediol; 1 M of imidazole, MES; 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.85 | α = 90 |
b = 87.85 | β = 90 |
c = 52.94 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
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 | PIXEL | DECTRIS PILATUS 2M | 2012-01-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9173 | Diamond | I04-1 |
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 | 1.5 | 45.31 | 99.4 | 0.106 | 0.106 | 13.8 | 6.8 | 64354 | 12.3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.5 | 1.54 | 99 | 0.808 | 3.2 | 6.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | SAD | THROUGHOUT | 1.5 | 45.31 | 61120 | 3218 | 99.36 | 0.1636 | 0.1623 | 0.1891 | RANDOM | 14.403 |
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] | |
0.05 | 0.05 | -0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.96 |
r_dihedral_angle_4_deg | 20.068 |
r_dihedral_angle_3_deg | 10.794 |
r_dihedral_angle_1_deg | 5.457 |
r_angle_refined_deg | 1.593 |
r_mcangle_it | 1.077 |
r_scbond_it | 0.926 |
r_mcbond_it | 0.616 |
r_chiral_restr | 0.111 |
r_bond_refined_d | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3110 |
Nucleic Acid Atoms | |
Solvent Atoms | 463 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
SHARP | phasing |