4A03
Crystal Structure of Mycobacterium tuberculosis DXR in complex with the antibiotic FR900098 and cofactor NADPH
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2JCZ | PDB ENTRY 2JCZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 10% (W/V) PEG 20000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.1 M MES/IMIDAZOLE, PH 6.5, AND 0.03 M EACH OF DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, TETRAETHYLENEGLYCOL AND PENTAETHYLENEGLYCOL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.66 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 110.51 | ¦Á = 90 |
b = 110.51 | ¦Â = 90 |
c = 137 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | 110 | CCD | ADSC QUANTUM 315r | 2010-09-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.65 | 42.21 | 99.8 | 0.09 | 14.4 | 7.8 | 101922 |
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 | 1.65 | 1.74 | 100 | 0.46 | 4.6 | 7.9 |
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 2JCZ | 1.65 | 42.21 | 96739 | 5087 | 99.77 | 0.19067 | 0.18931 | 0.21607 | RANDOM | 22.132 |
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] | |
-0.16 | -0.16 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.313 |
r_dihedral_angle_4_deg | 16.438 |
r_dihedral_angle_3_deg | 11.113 |
r_dihedral_angle_1_deg | 4.819 |
r_angle_refined_deg | 1.16 |
r_chiral_restr | 0.075 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5546 |
Nucleic Acid Atoms | |
Solvent Atoms | 529 |
Heterogen Atoms | 128 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |