4AT0
The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1D4C | PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY |
experimental model | PDB | 1E39 | PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY |
experimental model | PDB | 1KF6 | PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY |
experimental model | PDB | 1NEK | PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY |
experimental model | PDB | 1ZOY | PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 5.6 | CRYSTALS WERE OBTAINED FROM 200 MM AMMONIUM ACETATE, 100 MM SODIUM CITRATE PH 5.6 AND 30%(W/V) PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.06 | 59.8 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 99.233 | ¦Á = 90 |
b = 114.308 | ¦Â = 90 |
c = 110.161 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210r | MIRRORS | 2007-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM16 | ESRF | BM16 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.6 | 49.6 | 97 | 0.08 | 22.6 | 11.1 | 80282 | 16 |
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 | 1.6 | 1.69 | 83.8 | 0.32 | 4.7 | 6.1 |
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 | PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY | 1.6 | 39.65 | 75998 | 4019 | 96.94 | 0.15875 | 0.15786 | 0.17539 | RANDOM | 16.802 |
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] | |
-0.02 | 0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.61 |
r_dihedral_angle_4_deg | 15.35 |
r_dihedral_angle_3_deg | 11.26 |
r_dihedral_angle_1_deg | 5.367 |
r_angle_refined_deg | 1.436 |
r_angle_other_deg | 0.869 |
r_nbtor_refined | 0.307 |
r_nbd_other | 0.3 |
r_symmetry_vdw_refined | 0.249 |
r_nbd_refined | 0.225 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3598 |
Nucleic Acid Atoms | |
Solvent Atoms | 608 |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |