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)
TypeSourceAccession CodeDetails
experimental modelPDB 3CMF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4The 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
Matthews coefficientSolvent content
2.2344.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.892α = 90
b = 109.877β = 90
c = 128.961γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1.00NSLSX6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.73097.80.0490.04925.35769417694114.49
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.7692.90.350.353.54.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3CMF1.70124.3370.173560371793.510.1770.1750.205RANDOM18.375
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]
0.777-0.493-0.285
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.95
f_angle_d0.992
f_chiral_restr0.067
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5263
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms123

Software

Software
Software NamePurpose
PHENIXrefinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing