7WY4 | pdb_00007wy4

Structure of the CYP102A1 F87A Haem Domain with N-Enanthyl-L-Prolyl-L-Phenylalanine in complex with Styrene

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	PEG8000, Magnesium Chloride, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 126.65	β = 90
c = 148.75	γ = 90

Symmetry
Space Group	P 21 21 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	DECTRIS PILATUS3 X 6M		2019-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.45	48.22	100	0.113	0.122	0.998	9.74	6.761		187448			24.687

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.49	99.9		1.677	1.83	0.634	1.27	6.263

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	3WSP	1.45	48.22	187448	9838	99.97	0.1451	0.1433	0.14	0.1792	0.18	RANDOM	19.671

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]
-0.7			1.18		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.44
r_dihedral_angle_4_deg	17.014
r_dihedral_angle_3_deg	12.93
r_dihedral_angle_1_deg	6.597
r_angle_refined_deg	1.527
r_rigid_bond_restr	1.492
r_angle_other_deg	1.433
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.44
r_dihedral_angle_4_deg	17.014
r_dihedral_angle_3_deg	12.93
r_dihedral_angle_1_deg	6.597
r_angle_refined_deg	1.527
r_rigid_bond_restr	1.492
r_angle_other_deg	1.433
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7316
Nucleic Acid Atoms
Solvent Atoms	875
Heterogen Atoms	420

Software

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