7W9J | pdb_00007w9j

Crystal Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 (P450BM3) Heme Domain with N-Dodecanoyl-L-Homoserine Lactone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6K58

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		277	8.5%(w/v)PEG8000, 60 mM Magnesium Chloride, 75 mM Tris-HCl, 250 uM N-Dodecanoyl-L-Homoserine Lactone, 1%(v/v) Methanol

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.295	α = 90
b = 121.827	β = 90
c = 148.689	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 6M		2021-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000000	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	1.75	49.63	99.1	0.143	0.154	0.998	9.29	7.109		107242			30.641

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	1.75	1.85	97		1.41	1.527	0.581	1.47	6.727

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	6K58	1.75	49.63	101500	5329	99.36	0.1797	0.1781	0.19	0.2099	0.22	RANDOM	27.511

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]
-1.15			2.13		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.108
r_dihedral_angle_4_deg	14.714
r_dihedral_angle_3_deg	12.704
r_dihedral_angle_1_deg	6.482
r_angle_refined_deg	1.403
r_angle_other_deg	1.336
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.108
r_dihedral_angle_4_deg	14.714
r_dihedral_angle_3_deg	12.704
r_dihedral_angle_1_deg	6.482
r_angle_refined_deg	1.403
r_angle_other_deg	1.336
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7335
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	146

Software

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

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.