5JQ2 | pdb_00005jq2

Crystal structure of the Ru(bpy)2PhenA functionalized P450 BM3 L407C heme domain mutant in complex with N-palmitoylglycine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	150 mM MgCl2, 125 mM Na-MOPS, 20% PEG 3350, cryo: 30% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.88	α = 90
b = 112.54	β = 90
c = 156.36	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		2015-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

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	1.9	47.54	99.2	0.129	0.997	10.47	5		83423		-3	31.496

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	99.5		1.104	1.4

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	3NPL	2	47.54	68037	3581	99.13	0.1764	0.1742	0.18	0.2181	0.23	RANDOM	29.25

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]
-0.99			1.07		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.891
r_dihedral_angle_4_deg	15.433
r_dihedral_angle_3_deg	14.034
r_dihedral_angle_1_deg	6.633
r_mcangle_it	3.352
r_mcbond_it	2.231
r_mcbond_other	2.229
r_angle_refined_deg	1.817
r_angle_other_deg	1.039
r_chiral_restr	0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.891
r_dihedral_angle_4_deg	15.433
r_dihedral_angle_3_deg	14.034
r_dihedral_angle_1_deg	6.633
r_mcangle_it	3.352
r_mcbond_it	2.231
r_mcbond_other	2.229
r_angle_refined_deg	1.817
r_angle_other_deg	1.039
r_chiral_restr	0.113
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7367
Nucleic Acid Atoms
Solvent Atoms	491
Heterogen Atoms	216

Software

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

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.