7SNM | pdb_00007snm

Lanosterol-bound P450 domain of the CYP51-ferredoxin fusion protein from Methylococcus capsulatus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MI0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.1	298	Na-citrate tribasic dehydrate, PEG 8,000, dodecyltrimethylammonium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.21	α = 90
b = 206.16	β = 114.09
c = 81.43	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	PIXEL	CS-PAD CXI-1	Focussing mirrors	2021-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	1.000	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.55	74.45	99	0.065	0.998	13.4	7.1		67008

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.62	99.9		0.637	0.96	2.2	7.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6mi0	2.55	74.45	67008	3792	99.03	0.2073	0.2045	0.21	0.2458	0.26	RANDOM	54.83

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]
-0.53		-0.24	0.37		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.792
r_dihedral_angle_3_deg	17.175
r_dihedral_angle_4_deg	16.566
r_dihedral_angle_1_deg	6.677
r_rigid_bond_restr	6.01
r_angle_other_deg	1.421
r_angle_refined_deg	1.265
r_chiral_restr	0.064
r_gen_planes_other	0.016
r_gen_planes_refined	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.792
r_dihedral_angle_3_deg	17.175
r_dihedral_angle_4_deg	16.566
r_dihedral_angle_1_deg	6.677
r_rigid_bond_restr	6.01
r_angle_other_deg	1.421
r_angle_refined_deg	1.265
r_chiral_restr	0.064
r_gen_planes_other	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.009
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14130
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	296

Software

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