7V46

Crystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2 in complex with ortho-chlorotoluene.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CPT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	298	Na/K phosphate, glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.794	α = 90
b = 111.794	β = 90
c = 80.354	γ = 120

Symmetry
Space Group	P 32 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	RAYONIX MX300-HS		2019-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.9998	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.8	25	98.2	0.367	0.405	0.165	12.6	6.4		52983

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	97.6		0.656	0.709	0.267	0.853		6.3

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	1cpt	1.8	24.22	50352	2622	98.18	0.19	0.1884	0.2209	RANDOM	26.728

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]
-0.09	-0.04		-0.09		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.877
r_dihedral_angle_4_deg	15.999
r_dihedral_angle_3_deg	12.602
r_dihedral_angle_1_deg	6.476
r_angle_refined_deg	1.667
r_angle_other_deg	1.455
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.877
r_dihedral_angle_4_deg	15.999
r_dihedral_angle_3_deg	12.602
r_dihedral_angle_1_deg	6.476
r_angle_refined_deg	1.667
r_angle_other_deg	1.455
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3417
Nucleic Acid Atoms
Solvent Atoms	558
Heterogen Atoms	56

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	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.