3QWH | pdb_00003qwh

Crystal structure of the 17beta-hydroxysteroid dehydrogenase from Cochliobolus lunatus in complex with NADPH and kaempferol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QWF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	293	30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V) Crystals soaked in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 2MM KAEMPFEROL, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.95	α = 90
b = 116.64	β = 102.54
c = 70.24	γ = 90

Symmetry
Space Group	P 1 21 1

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	MAR CCD 165 mm	PT-COATED TOROIDAL MIRROR	2008-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0	ELETTRA	5.2R

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	2.61	39.1	93.9	0.061	0.061	12.5	3.5	28133	28133		-3	46

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	2.61	2.75	75.5		0.187	0.187	5	2.6	3279

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	3QWF	2.62	39.1	28102	28102	1410	94.3	0.17188	0.17188	0.168	0.18	0.24	0.24	RANDOM	39.801

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]
0.01			-0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.253
r_dihedral_angle_3_deg	14.868
r_dihedral_angle_4_deg	12.592
r_dihedral_angle_1_deg	5.651
r_scangle_it	1.664
r_angle_refined_deg	1.246
r_scbond_it	1
r_mcangle_it	0.625
r_mcbond_it	0.32
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.253
r_dihedral_angle_3_deg	14.868
r_dihedral_angle_4_deg	12.592
r_dihedral_angle_1_deg	5.651
r_scangle_it	1.664
r_angle_refined_deg	1.246
r_scbond_it	1
r_mcangle_it	0.625
r_mcbond_it	0.32
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7843
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	262

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.