2IPF
Crystal structure of 17alpha-hydroxysteroid dehydrogenase 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 | 2HEJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | hanging drop | 8 | 277 | PEG-6000 18%, 0.1M TRIS, 5% MPD, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.23 | α = 90 |
b = 97.4 | β = 99.26 |
c = 79.46 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 IIC | mirrors | 2006-05-06 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | M |
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) | 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 | 1.85 | 19.64 | 94.5 | 0.085 | 0.075 | 16.22 | 5 | 63097 | 59634 | 23.231 |
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 | 1.85 | 1.9 | 89.4 | 0.366 | 0.369 | 3.4 | 3.4 | 4480 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 2HEJ | 1.85 | 19.64 | 63097 | 59634 | 3032 | 95.1 | 0.171 | 0.2 | RANDOM | 18.2 |
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] | |
3.09 | -2.43 | -1.33 | -1.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 2.51 |
c_scbond_it | 1.8 |
c_mcangle_it | 1.45 |
c_angle_deg | 1.2 |
c_mcbond_it | 1.07 |
c_improper_angle_d | 0.81 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5110 |
Nucleic Acid Atoms | |
Solvent Atoms | 692 |
Heterogen Atoms | 182 |
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 |
MOLREP | phasing |