4C3Y
Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 2% (V/V) PEG (POLYETHYLENE GLYCOL) 400, 0.1 M HEPES (4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID) BUFFER PH 7.5, 2.0 M AMMONIUM SULFATE. SITTING DROP. TEMPERATURE 293 K. THE PROTEIN SOLUTION SAMPLE WAS INCUBATED WITH 1,4-ANDROSTADIENE-3,17-DIONE POWDER ON ICE FOR 3 H PRIOR TO THE CRYSTALLIZATION EXPERIMENT. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.747 | α = 90 |
b = 132.142 | β = 90 |
c = 363.597 | 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 | CCD | ADSC CCD | 2011-11-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 2.3 | 49.42 | 99.5 | 0.13 | 7.2 | 4.6 | 229728 |
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 | 2.3 | 2.42 | 96.7 | 0.72 | 1.9 | 4.5 |
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 | OTHER | THROUGHOUT | NONE | 2.3 | 49.42 | 217960 | 11485 | 99.65 | 0.21236 | 0.21045 | 0.24882 | RANDOM | 41.418 |
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] | |
0.26 | 0.03 | -0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.845 |
r_dihedral_angle_4_deg | 19.837 |
r_dihedral_angle_3_deg | 14.761 |
r_dihedral_angle_1_deg | 5.667 |
r_angle_other_deg | 2.743 |
r_angle_refined_deg | 1.415 |
r_chiral_restr | 0.072 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 29620 |
Nucleic Acid Atoms | |
Solvent Atoms | 1414 |
Heterogen Atoms | 674 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |