4XE3

OleP, the cytochrome P450 epoxidase from Streptomyces antibioticus involved in Oleandomycin biosynthesis: functional analysis and crystallographic structure in complex with clotrimazole.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y46	PDB entry 2Y46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.6 M Ammonium Sulphate, 0.1 M HEPES Sodium Salt pH 7.5, 2% (w/v) PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.937	α = 90
b = 117.379	β = 90
c = 174.664	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	PSI PILATUS 6M		2010-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.65	50	99.1	0.094	0.102	17.32	6.88		34700		-3	56.435

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.81	95.4		0.86	0.941	2.1

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2Y46	2.65	48.76	34700	1744	99.13	0.2095	0.2068	0.2596	RANDOM	58.33

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]
-3.04			-1.05		4.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.434
r_dihedral_angle_3_deg	21.312
r_dihedral_angle_4_deg	18.713
r_dihedral_angle_1_deg	7.713
r_angle_refined_deg	1.772
r_angle_other_deg	0.895
r_chiral_restr	0.197
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.434
r_dihedral_angle_3_deg	21.312
r_dihedral_angle_4_deg	18.713
r_dihedral_angle_1_deg	7.713
r_angle_refined_deg	1.772
r_angle_other_deg	0.895
r_chiral_restr	0.197
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6142
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

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.