3G1R
Crystal structure of human liver 5beta-reductase (AKR1D1) in complex with NADP and Finasteride. Resolution 1.70 A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CMF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | The ternary complexes of AKR1D1-NADP+-finasteride was crystallized by the hanging drop vapor diffusion method at 4 C. Drops containing 3.0 L of enzyme solution [5.0 mg/mL AKR1D1, 2.0 mM NADP+, 0.5 mM finasteride, 10.0 mM Tris (pH 7.4)] and 4.0 L of precipitant buffer [0.1 M TRIS-HCl (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% iso-propanol] were equilibrated against a 1 mL reservoir of precipitant buffer. Crystals of the AKR1D1-NADP+-finasteride, complex were soaked for 24 hours in the same mother liquor solution augmented with 2.0 mm NADP+, 2.0 mM finasteride and 30% iso-propanol, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.892 | α = 90 |
b = 109.877 | β = 90 |
c = 128.961 | 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 QUANTUM 210 | 2007-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.00 | NSLS | X6A |
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 | 1.7 | 30 | 97.8 | 0.049 | 0.049 | 25.3 | 5 | 76941 | 76941 | 14.49 |
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) | ||||||||||
1.7 | 1.76 | 92.9 | 0.35 | 0.35 | 3.5 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FOURIER SYNTHESIS | THROUGHOUT | 3CMF | 1.701 | 24.337 | 0.1 | 73560 | 3717 | 93.51 | 0.177 | 0.175 | 0.205 | RANDOM | 18.375 |
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] | |
0.777 | -0.493 | -0.285 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.95 |
f_angle_d | 0.992 |
f_chiral_restr | 0.067 |
f_bond_d | 0.006 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5263 |
Nucleic Acid Atoms | |
Solvent Atoms | 754 |
Heterogen Atoms | 123 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
CNS | refinement |
ADSC | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |