7WG0 | pdb_00007wg0

Structure of the Manganese Protoporphyrin IX-Reconstituted CYP102A1 Heme Domain with N-palmitoyl-L-phenylalanine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	tris(hydroxymethyl)aminomethane, Magnesium chloride, PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.78	α = 90
b = 127.89	β = 90
c = 148.67	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 PILATUS 6M		2019-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	148.67	100	0.996	9.22	48.16		57834

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	6.6			0.674

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	1JPZ	2.2	48.52	54760	3001	99.98	0.2113	0.2084	0.21	0.2667	0.27	RANDOM	34.791

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]
-0.52			0.95		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.642
r_dihedral_angle_4_deg	16.214
r_dihedral_angle_3_deg	14.966
r_dihedral_angle_1_deg	7.364
r_angle_refined_deg	2.299
r_angle_other_deg	1.335
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.642
r_dihedral_angle_4_deg	16.214
r_dihedral_angle_3_deg	14.966
r_dihedral_angle_1_deg	7.364
r_angle_refined_deg	2.299
r_angle_other_deg	1.335
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7324
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	144

Software

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