2IPJ | pdb_00002ipj

Crystal structure of h3alpha-hydroxysteroid dehydrogenase type 3 mutant Y24A in complex with NADP+ and epi-testosterone

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	5.6	277	PEG-4000 22%, 0.1M NaCitrate, pH 5.6, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.788	α = 90
b = 144.788	β = 90
c = 203.885	γ = 120

Symmetry
Space Group	H 3 2

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 130 mm		2005-12-03	M	SINGLE WAVELENGTH
2	1	x-ray		M
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	1.000	ESRF	BM30A

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	1.8	19.98	99.7	0.068	0.066	18.29	7.4	75962	75736			29.947

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	1.8	1.9	97.6		0.278	0.458	4.4	7.4	11281

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	2HDJ	1.8	19.98	74951	3811	99.7	0.204	0.2	0.228	0.23	RANDOM	28.6

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]
1.65	1.49		1.65		-3.31

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.2
c_scangle_it	2.31
c_mcangle_it	1.73
c_scbond_it	1.69
c_angle_deg	1.3
c_mcbond_it	1.16
c_improper_angle_d	0.86
c_bond_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5132
Nucleic Acid Atoms
Solvent Atoms	613
Heterogen Atoms	193

Software

Software
Software Name	Purpose
XSCALE	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction
XSCALE	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.