3G1R | pdb_00003g1r

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)
Type	Source	Accession Code	Details
experimental model	PDB	3CMF

Crystallization

Crystalization Experiments
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
Matthews coefficient	Solvent content
2.23	44.88

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
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
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.00	NSLS	X6A

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)	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
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
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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.18	0.205	0.17	RANDOM	18.375

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
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
Non-Hydrogen Atoms	Number
Protein Atoms	5263
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	123

Software

Software
Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.