4XTY
Mycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor 63 with Fluorine in place of 2'OH
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RUX | PDB entry 3RUX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 17-24% PEG2000 MME, 100 mM Tris, pH 8.5, 100 mM triethylamine N-oxide |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.408 | α = 90 |
b = 68.731 | β = 90 |
c = 114.488 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 6M | 2013-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.000 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 114.5 | 99.8 | 0.055 | 21.6 | 6.5 | 47014 | 19.5494820663 |
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 | 1.8 | 1.806 | 98.6 | 0.273 | 6 | 6.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 3RUX | 1.80002665982 | 36.1414570832 | 1.33646189146 | 46947 | 2376 | 99.6286235729 | 0.178825293314 | 0.177025783935 | 0.211615751309 | 21.9364579023 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.2142368739 |
f_angle_d | 1.294593722 |
f_chiral_restr | 0.0496579037701 |
f_bond_d | 0.00721772399406 |
f_plane_restr | 0.00526579353473 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3908 |
Nucleic Acid Atoms | |
Solvent Atoms | 332 |
Heterogen Atoms | 76 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SCALA | data scaling |