4OP0
Crystal structure of biotin protein ligase (RV3279C) of Mycobacterium tuberculosis, complexed with biotinyl-5'-AMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CGH | PDB ENTRY 2CGH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 293 | 0.1 M Tris-HCl, pH 7.8, 0.2 M lithium sulfate, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.54 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 41.737 | ¦Á = 90 |
b = 75.406 | ¦Â = 97.92 |
c = 77.599 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | CCD | MAR CCD 165 mm | mirrors: 1: Rh-coated, zerodur, vertical focusing possible, 2: Rh-coated, zerodur, vertically focusing | 2006-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.9762 | EMBL/DESY, HAMBURG | BW7A |
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 | 1.7 | 31.36 | 97.4 | 0.098 | 15.6 | 12 | 51119 | 2 | 2 | 24.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.7 | 1.8 | 95.9 | 0.526 | 3.25 | 7.1 | 7904 |
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 | PDB ENTRY 2CGH | 1.7 | 31.36 | 48546 | 2550 | 100 | 0.194 | 0.192 | 0.242 | RANDOM | 28.938 |
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] | |
-0.39 | -0.58 | 1.37 | -1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.506 |
r_dihedral_angle_4_deg | 18.981 |
r_dihedral_angle_3_deg | 13.586 |
r_dihedral_angle_1_deg | 6.753 |
r_scangle_it | 3.199 |
r_scbond_it | 2.227 |
r_angle_refined_deg | 1.749 |
r_mcangle_it | 1.401 |
r_angle_other_deg | 1.001 |
r_mcbond_it | 0.916 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3776 |
Nucleic Acid Atoms | |
Solvent Atoms | 372 |
Heterogen Atoms | 81 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |