3VGN | pdb_00003vgn

Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 3-fluoro-4-nitrophenol

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	1.4M Ammonium sulphate, 6-7% 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.483	α = 90
b = 72.315	β = 90
c = 95.282	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate		2005-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.82656	SSRL	BL1-5

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	1.3	35	91.3	0.076	10.3	4.1	55738	55738		-3	13.4

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)
1	1.3	1.35	78.7		0.738		3.7	4700

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	3FZW	1.3	33.25	55738	55689	2814	91.21	0.1717	0.1717	0.1694	0.17	0.218	0.22	RANDOM	22.6604

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]
1.23			-0.07		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.958
r_sphericity_free	24.155
r_dihedral_angle_4_deg	17.583
r_dihedral_angle_3_deg	14.928
r_sphericity_bonded	14.304
r_rigid_bond_restr	7.855
r_dihedral_angle_1_deg	6.081
r_angle_refined_deg	1.528
r_chiral_restr	0.094
r_bond_refined_d	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.958
r_sphericity_free	24.155
r_dihedral_angle_4_deg	17.583
r_dihedral_angle_3_deg	14.928
r_sphericity_bonded	14.304
r_rigid_bond_restr	7.855
r_dihedral_angle_1_deg	6.081
r_angle_refined_deg	1.528
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1960
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	22

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	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.