3UAS | pdb_00003uas

Cytochrome P450 2B4 covalently bound to the mechanism-based inactivator 9-ethynylphenanthrene

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.1 M Tris, 20% (w/v) PEG 3000, 0.2 M calcium acetate, pH 7.0, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.155	α = 90
b = 90.155	β = 90
c = 148.623	γ = 120

Symmetry
Space Group	P 31 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	APEX II CCD		2011-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER	1.54

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	2.939	78.08	99.8	0.128	0.128	12.73	7.4	15475	15444

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	2.939	2.96	92.6		0.395	2.14	3.61	174

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	PDB ENTRY 1SUO	2.939	78.08	15435	15379	765	99.64	0.2455	0.2455	0.2429	0.24	0.2961	0.28	RANDOM	28.641

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]
-0.9	-0.45		-0.9		1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.467
r_dihedral_angle_4_deg	14.664
r_dihedral_angle_3_deg	14.55
r_dihedral_angle_1_deg	4.774
r_angle_refined_deg	0.952
r_scangle_it	0.893
r_mcangle_it	0.501
r_scbond_it	0.486
r_mcbond_it	0.269
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.467
r_dihedral_angle_4_deg	14.664
r_dihedral_angle_3_deg	14.55
r_dihedral_angle_1_deg	4.774
r_angle_refined_deg	0.952
r_scangle_it	0.893
r_mcangle_it	0.501
r_scbond_it	0.486
r_mcbond_it	0.269
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3696
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	116

Software

Software
Software Name	Purpose
SAINT	data scaling
XPREP	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	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.