4TVO
Structure of Malate Dehydrogenase from Mycobacterium tuberculosis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293.15 | Malate dehydrogenase crystals grew in 0.2M Lithium Sulfate monohydrate, 0.1M Tris-HCl pH=8.5, 30% w/v PEG 4000 in the 50/50 protein/reservoir-ratio drop of 1 microlitre.. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.606 | α = 90 |
b = 79.307 | β = 90 |
c = 155.513 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS PILATUS 6M-F | 2012-05-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.98 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.5 | 77.76 | 99.44 | 13.57 | 3.3 | 103872 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 1.5 | 77.76 | 98672 | 5200 | 99.4 | 0.1673 | 0.16595 | 0.19274 | RANDOM | 20.321 |
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] | |
-0.21 | 1.33 | -1.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.796 |
r_dihedral_angle_4_deg | 15.993 |
r_dihedral_angle_3_deg | 10.945 |
r_dihedral_angle_1_deg | 6.235 |
r_long_range_B_refined | 6.222 |
r_long_range_B_other | 6.07 |
r_scangle_other | 4.804 |
r_scbond_it | 3.253 |
r_scbond_other | 3.229 |
r_mcangle_it | 2.704 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4728 |
Nucleic Acid Atoms | |
Solvent Atoms | 473 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |