2VZZ
Crystal structure of Rv0802c from Mycobacterium tuberculosis in Complex with Succinyl-CoA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VZY | PDB ENTRY 2VZY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | PROTEIN AT 8 MG/ML IN 20 MM TEA PH 8.5, 100 MM AMMONIUM SULFATE, 1 MM EDTA, 1 MM DTT, 2 MM COA, 4 MM SUCCOA CRYSTALLIZED IN 1 M LICL, 100 MM HEPES PH 7.0. CRYOPROTECTED IN PRECIPITANT SOLUTION PLUS 20 MM SUCCOA AND 20% GLYCEROL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.165 | α = 90 |
b = 135.172 | β = 90 |
c = 164.077 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | 93 | IMAGE PLATE | RIGAKU IMAGE PLATE | OSMIC BLUE CONFOCAL | 2004-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
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 | 2.3 | 104 | 95.9 | 0.06 | 15.3 | 3.5 | 53759 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.3 | 2.38 | 92.8 | 0.2 | 4.8 | 3 |
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 2VZY | 2.3 | 104.26 | 51029 | 2730 | 95.8 | 0.172 | 0.169 | 0.222 | RANDOM | 19.81 |
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] | |
0.33 | 1.26 | -1.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.199 |
r_dihedral_angle_4_deg | 16.542 |
r_dihedral_angle_3_deg | 14.568 |
r_dihedral_angle_1_deg | 5.914 |
r_scangle_it | 3.623 |
r_scbond_it | 2.247 |
r_angle_refined_deg | 1.684 |
r_mcangle_it | 1.321 |
r_mcbond_it | 0.779 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6763 |
Nucleic Acid Atoms | |
Solvent Atoms | 413 |
Heterogen Atoms | 220 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |