3NM2 | pdb_00003nm2

Crystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from Pseudomonas Testosteroni (tKSI)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8CHO	PDB ENTRY 8CHO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	2.0 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 1 mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.356	α = 90
b = 59.356	β = 90
c = 141.974	γ = 120

Symmetry
Space Group	P 65 2 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	MARMOSAIC 325 mm CCD		2010-03-25		SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2010-03-24		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	1.887	29.678	99.6	0.078	21.6	13.2	12614	12614			29.1

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	1.887	1.99	97.2		0.983	0.983	0.8	10.8	1741

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 8CHO	1.887	29.678	12563	12563	610	99.53	0.2048	0.2048	0.2024	0.21	0.2536	0.26	RANDOM	37.019

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]
1.41	0.71		1.41		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_4_deg	17.854
r_dihedral_angle_3_deg	15.211
r_dihedral_angle_1_deg	6.952
r_scangle_it	6.085
r_scbond_it	3.858
r_mcangle_it	2.301
r_angle_refined_deg	2.137
r_mcbond_it	1.39
r_chiral_restr	0.152

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_4_deg	17.854
r_dihedral_angle_3_deg	15.211
r_dihedral_angle_1_deg	6.952
r_scangle_it	6.085
r_scbond_it	3.858
r_mcangle_it	2.301
r_angle_refined_deg	2.137
r_mcbond_it	1.39
r_chiral_restr	0.152
r_bond_refined_d	0.026
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	938
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
Web-Ice	data collection
XDS	data reduction

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.