3M8C

Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with Equilenin Bound

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop	7.2	298	1.4 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.312	α = 90
b = 64.312	β = 90
c = 506.174	γ = 120

Symmetry
Space Group	P 61 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	PIXEL	DECTRIS PILATUS 6M		2010-01-16		SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2010-01-06		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.98	SSRL	BL9-1
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.98	SSRL	BL9-2

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	2.1	33.63	99.2	0.094	20.6	11.7	38027	38027			24.5

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)
	2.1	2.21	94.8		0.416	4.9	8.1	5131

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	8CHO	2.1	84.36	38027	37837	1895	99.15	0.169	0.169	0.166	0.222	RANDOM	26.739

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]
1.02	0.51		1.02		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.228
r_dihedral_angle_4_deg	20.81
r_dihedral_angle_3_deg	15.56
r_dihedral_angle_1_deg	6.551
r_scangle_it	4.845
r_scbond_it	3.223
r_mcangle_it	2.018
r_angle_refined_deg	1.989
r_mcbond_it	1.17
r_chiral_restr	0.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.228
r_dihedral_angle_4_deg	20.81
r_dihedral_angle_3_deg	15.56
r_dihedral_angle_1_deg	6.551
r_scangle_it	4.845
r_scbond_it	3.223
r_mcangle_it	2.018
r_angle_refined_deg	1.989
r_mcbond_it	1.17
r_chiral_restr	0.146
r_bond_refined_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3756
Nucleic Acid Atoms
Solvent Atoms	466
Heterogen Atoms	137

Software

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