1XF0 | pdb_00001xf0

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 (AKR1C3) complexed with delta4-androstene-3,17-dione and NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ASF	PDB ENTRY 1ASF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	PEG 8000, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.579	α = 90
b = 110.579	β = 90
c = 56.886	γ = 120

Symmetry
Space Group	P 63

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 4		2000-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.9511	NSLS	X8C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50	99.6	0.143	9.91	8.1	27053	26940		2	27.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	98.6		0.488	2.46	3.6

Refinement

Statistics
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-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ASF	2	36.2	27053	25590	1350	99.64	0.191	0.17284	0.17013	0.17	0.22488	0.22	RANDOM	18.318

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.814
r_dihedral_angle_4_deg	18.108
r_dihedral_angle_3_deg	12.804
r_dihedral_angle_1_deg	6.284
r_scangle_it	3.645
r_scbond_it	2.464
r_angle_refined_deg	2.408
r_mcangle_it	1.571
r_mcbond_it	1.041
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.814
r_dihedral_angle_4_deg	18.108
r_dihedral_angle_3_deg	12.804
r_dihedral_angle_1_deg	6.284
r_scangle_it	3.645
r_scbond_it	2.464
r_angle_refined_deg	2.408
r_mcangle_it	1.571
r_mcbond_it	1.041
r_nbtor_refined	0.31
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.153
r_symmetry_vdw_refined	0.15
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2538
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	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.