2IPJ
Crystal structure of h3alpha-hydroxysteroid dehydrogenase type 3 mutant Y24A in complex with NADP+ and epi-testosterone
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2HDJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | hanging drop | 5.6 | 277 | PEG-4000 22%, 0.1M NaCitrate, pH 5.6, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.82 | 56.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 144.788 | α = 90 |
b = 144.788 | β = 90 |
c = 203.885 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 | MAR CCD 130 mm | 2005-12-03 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | M | |||||||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 1.000 | ESRF | BM30A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.8 | 19.98 | 99.7 | 0.068 | 0.066 | 18.29 | 7.4 | 75962 | 75736 | 29.947 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1,2 | 1.8 | 1.9 | 97.6 | 0.278 | 0.458 | 4.4 | 7.4 | 11281 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2HDJ | 1.8 | 19.98 | 74951 | 3811 | 99.7 | 0.204 | 0.228 | RANDOM | 28.6 |
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] | |
1.65 | 1.49 | 1.65 | -3.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.2 |
c_scangle_it | 2.31 |
c_mcangle_it | 1.73 |
c_scbond_it | 1.69 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.16 |
c_improper_angle_d | 0.86 |
c_bond_d | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5132 |
Nucleic Acid Atoms | |
Solvent Atoms | 613 |
Heterogen Atoms | 193 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data processing |
CNS | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
XDS | data reduction |
XSCALE | data scaling |