3SC4
Crystal structure of a Short chain dehydrogenase (A0QTM2 homolog) Mycobacterium thermoresistibile
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KVO | PDB ENTRY 3KVO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | Internal tracking number 220646H3. Focus screen based on JCSG E2. 2 M ammonium sulfate, 0.1 M cacodylate, pH 6.54, 200 mM sodium chloride. MythA.01365.a.A1 PW28688 at 27.8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.7 | 67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.49 | α = 90 |
b = 111.49 | β = 90 |
c = 124.88 | γ = 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 | CCD | ADSC QUANTUM 315 | 2011-05-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | ALS | 5.0.1 |
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 | 2.5 | 48.28 | 99.8 | 0.101 | 21.89 | 9.3 | 30482 | 30423 | -3 | 37.017 |
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 | 2.5 | 2.56 | 100 | 0.564 | 4.4 | 9.2 | 2240 |
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 3KVO | 2.5 | 48.28 | 30393 | 2343 | 99.72 | 0.181 | 0.178 | 0.22 | RANDOM | 27.608 |
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] | |
-0.45 | -0.22 | -0.45 | 0.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.398 |
r_dihedral_angle_4_deg | 17.257 |
r_dihedral_angle_3_deg | 14.984 |
r_dihedral_angle_1_deg | 6.567 |
r_scangle_it | 3.052 |
r_scbond_it | 1.837 |
r_angle_refined_deg | 1.46 |
r_mcangle_it | 1.153 |
r_angle_other_deg | 0.906 |
r_mcbond_it | 0.606 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4113 |
Nucleic Acid Atoms | |
Solvent Atoms | 150 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |