3MZS | pdb_00003mzs

Crystal Structure of Cytochrome P450 CYP11A1 in complex with 22-hydroxy-cholesterol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K9V	PDB entry 3K9V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	285	16% PEG 1000, 10% Jeffamine ED-2001, 20% glycerol, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.45	α = 90
b = 94.63	β = 89.96
c = 113.5	γ = 90

Symmetry
Space Group	P 1 21 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	Rh coated flat mirror	2010-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979	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	2.5	113.5	95.5	0.068	0.068	5.8	2	76291	76291			74.2

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)
	2.5	2.64	97.5		0.444	0.444	1.6	2	11367

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 (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 3K9V	2.5	60.01	76259	72447	3812	94.9	0.266	0.266	0.27	0.281	0.28	RANDOM	65.893

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]
-66.06		-11.86	9.17		56.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.73
r_dihedral_angle_4_deg	19.327
r_dihedral_angle_3_deg	18.5
r_dihedral_angle_1_deg	7.711
r_scangle_it	3.953
r_scbond_it	2.511
r_mcangle_it	1.788
r_angle_refined_deg	1.684
r_mcbond_it	0.98
r_chiral_restr	0.149

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.73
r_dihedral_angle_4_deg	19.327
r_dihedral_angle_3_deg	18.5
r_dihedral_angle_1_deg	7.711
r_scangle_it	3.953
r_scbond_it	2.511
r_mcangle_it	1.788
r_angle_refined_deg	1.684
r_mcbond_it	0.98
r_chiral_restr	0.149
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15616
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	304

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.