3FVE
Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BWZ | PDB entry 1BWZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 9.5 | 291 | 1.9 M (NH4)H2PO4, 0.1 M bis-tris propane, pH 9.5, 2.5% glycerol, vapor diffusion, temperature 291K, VAPOR DIFFUSION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.68 | 66.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.64 | α = 90 |
b = 183.64 | β = 90 |
c = 45.21 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | 100 | CCD | ADSC QUANTUM Q315r | 2008-09-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.976 | ESRF | ID29 |
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 | 2.59 | 45.22 | 99.7 | 0.086 | 0.086 | 13.2 | 14430 | 14430 | 64.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.59 | 2.73 | 98.4 | 0.758 | 0.758 | 3.8 | 13 | 2020 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1BWZ | 2.6 | 45 | 14341 | 14341 | 722 | 99.97 | 0.226 | 0.226 | 0.224 | 0.254 | RANDOM | 38.103 |
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] | |
-1.06 | -0.53 | -1.06 | 1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.896 |
r_dihedral_angle_3_deg | 18.3 |
r_dihedral_angle_4_deg | 17.41 |
r_dihedral_angle_1_deg | 5.639 |
r_scangle_it | 1.609 |
r_angle_refined_deg | 1.362 |
r_scbond_it | 0.966 |
r_mcangle_it | 0.817 |
r_mcbond_it | 0.458 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2003 |
Nucleic Acid Atoms | |
Solvent Atoms | 38 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |
SCALA | data scaling |