4FA3

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with (R)-1-(naphthalen-2-ylsulfonyl)piperidine-3-carboxylic acid (86)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FGB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	20% PEG3350, 0.2 M sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.127	α = 90
b = 63.469	β = 90
c = 96.445	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	RIGAKU SATURN 944+	Varimax HF Optics	2010-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54182

Data Collection

Overall
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	2.2	18.68	97.6	0.096		2.9	17915	17915

Highest Resolution Shell
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	2.2	2.28	93.5		0.342	1.9	2.4	1656

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2FGB	2.2	18.68	51579	17000	915	97.43	0.21115	0.20772	0.27808	RANDOM	23.701

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]
-1.08			-0.63		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.901
r_dihedral_angle_3_deg	15.748
r_dihedral_angle_4_deg	14.28
r_dihedral_angle_1_deg	6.793
r_scangle_it	3.724
r_scbond_it	2.571
r_angle_refined_deg	1.848
r_mcangle_it	1.578
r_angle_other_deg	1.045
r_mcbond_it	0.906

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.901
r_dihedral_angle_3_deg	15.748
r_dihedral_angle_4_deg	14.28
r_dihedral_angle_1_deg	6.793
r_scangle_it	3.724
r_scbond_it	2.571
r_angle_refined_deg	1.848
r_mcangle_it	1.578
r_angle_other_deg	1.045
r_mcbond_it	0.906
r_mcbond_other	0.261
r_chiral_restr	0.12
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2414
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	78

Software

Software
Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement

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.