3KE7 | pdb_00003ke7

Crystal structure of putative ketosteroid isomerase (YP_001303366.1) from Parabacteroides distasonis ATCC 8503 at 1.45 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	2.4000M (NH4)2SO4, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.66	α = 90
b = 60.897	β = 102.3
c = 52.28	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-04-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97805,0.97862	SSRL	BL11-1

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	1.45	27.077	98.5	0.065	0.065	9.8	2.2		39881			13.881

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	1.45	1.49	97		0.354	0.354	2.1	2.2	2872

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MAD	THROUGHOUT	1.45	27.077	39881	2004	98.25	0.153	0.152	0.16	0.182	0.18	RANDOM	13.291

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]
0.37		0.61	-0.47		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.952
r_dihedral_angle_4_deg	24.222
r_dihedral_angle_3_deg	12.212
r_scangle_it	5.784
r_dihedral_angle_1_deg	4.993
r_scbond_it	4.164
r_mcangle_it	2.897
r_mcbond_it	1.799
r_angle_refined_deg	1.644
r_angle_other_deg	0.917

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.952
r_dihedral_angle_4_deg	24.222
r_dihedral_angle_3_deg	12.212
r_scangle_it	5.784
r_dihedral_angle_1_deg	4.993
r_scbond_it	4.164
r_mcangle_it	2.897
r_mcbond_it	1.799
r_angle_refined_deg	1.644
r_angle_other_deg	0.917
r_mcbond_other	0.474
r_chiral_restr	0.096
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2129
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	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.