2VVO
Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with alpha d-allose 6-phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1USL | PDB ENTRY 1USL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 1M TRI-NA CITRATE, 0.1M NA CACODYLATE PH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 152.744 | ¦Á = 90 |
b = 92.501 | ¦Â = 98.92 |
c = 60.967 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 110 | CCD | ADSC CCD | 2006-03-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
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 | 1.85 | 60.19 | 91.7 | 0.07 | 12.8 | 4.2 | 65360 | 2.6 | 23.4 |
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 | 1.85 | 1.95 | 61.8 | 0.51 | 2.6 | 4.1 |
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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1USL | 1.85 | 40 | 2.6 | 62048 | 3307 | 91.5 | 0.162 | 0.16 | 0.196 | RANDOM | 18.56 |
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] | |
-0.57 | -0.17 | -0.39 | 0.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.274 |
r_dihedral_angle_4_deg | 17.016 |
r_dihedral_angle_3_deg | 13.148 |
r_dihedral_angle_1_deg | 6.043 |
r_scangle_it | 3.675 |
r_scbond_it | 2.463 |
r_angle_refined_deg | 1.441 |
r_mcangle_it | 1.361 |
r_mcbond_it | 1.082 |
r_angle_other_deg | 1.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5897 |
Nucleic Acid Atoms | |
Solvent Atoms | 420 |
Heterogen Atoms | 80 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |