1MRQ
Crystal structure of human 20alpha-HSD in ternary complex with NADP and 20alpha-hydroxy-progesterone
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1J96 | PDB ENTRY 1J96 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | PEG 4000, HEPES, ammonium sulfate, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.65 | α = 90 |
b = 83.54 | β = 90 |
c = 100.68 | 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 | IMAGE PLATE | RIGAKU RAXIS | mirrors | 2002-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 1.59 | 20 | 95.6 | 0.056 | 23.8 | 6.7 | 43980 | 1 |
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 | 1.59 | 1.62 | 60.6 | 0.172 | 6.1 | 2.4 | 1482 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | PDB ENTRY 1J96 | 1.59 | 20 | 1 | 44183 | 41981 | 2202 | 96.45 | 0.17291 | 0.19444 | RANDOM | 7.686 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 10.315 |
r_dihedral_angle_1_deg | 4.319 |
r_scangle_it | 2.596 |
r_scbond_it | 1.571 |
r_angle_refined_deg | 1.25 |
r_mcangle_it | 0.871 |
r_mcbond_it | 0.459 |
r_nbd_refined | 0.198 |
r_symmetry_vdw_refined | 0.189 |
r_xyhbond_nbd_refined | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2593 |
Nucleic Acid Atoms | |
Solvent Atoms | 321 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
AMoRE | phasing |
REFMAC | refinement |
XDS | data scaling |