5Y8O
Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD + 3-Hydroxy propionate (3-HP)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3OBB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 295 | 0.02M MgCl2.6H2O, 0.1M HEPES pH 7.5, 22% w/v polyacrylic acid sodium salt 5100 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.47 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 129.06 | ¦Á = 90 |
b = 129.06 | ¦Â = 90 |
c = 70.13 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 65 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2017-08-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 2.05 | 111.77 | 99 | 0.16 | 6 | 3.6 | 41484 |
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 | 2.05 | 2.16 | 99 | 0.16 | 6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3OBB | 2.05 | 111.77 | 39313 | 2095 | 98.89 | 0.17819 | 0.1757 | 0.22508 | RANDOM | 23.308 |
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] | |
0.11 | 0.05 | 0.11 | -0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.452 |
r_dihedral_angle_4_deg | 20.566 |
r_dihedral_angle_3_deg | 14.957 |
r_long_range_B_refined | 7.596 |
r_long_range_B_other | 7.539 |
r_dihedral_angle_1_deg | 6.1 |
r_scangle_other | 3.917 |
r_scbond_it | 2.501 |
r_scbond_other | 2.499 |
r_mcangle_other | 2.331 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4097 |
Nucleic Acid Atoms | |
Solvent Atoms | 518 |
Heterogen Atoms | 87 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |