6H08

The crystal structure of engineered cytochrome c peroxidase from Saccharomyces cerevisiae with a His175Me-His proximal ligand substitution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	5 mM cobalt(II) chloride hexahydrate, 5 mM cadmium chloride hemi(pentahydrate), 5 mM magnesium chloride hexahydrate, 5 mM nickel(II) chloride hexahydrate, 0.1 M HEPES pH 7.5 and 12% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.92	α = 90
b = 106.77	β = 90
c = 163.72	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-F		2018-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9159	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.9	81.86	99.11	0.052	0.057	0.022	0.999	19.2	6.6		100412			33.84

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	97.15		0.392	0.425	0.163	0.966	4.3	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.9	81.86	95376	4974	99.05	0.1796	0.1783	0.2054	RANDOM	33.345

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]
4.54			-3.44		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.743
r_dihedral_angle_4_deg	23.708
r_dihedral_angle_3_deg	12.266
r_dihedral_angle_1_deg	5.697
r_angle_refined_deg	1.222
r_angle_other_deg	0.919
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_other	0.008
r_gen_planes_refined	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.743
r_dihedral_angle_4_deg	23.708
r_dihedral_angle_3_deg	12.266
r_dihedral_angle_1_deg	5.697
r_angle_refined_deg	1.222
r_angle_other_deg	0.919
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7222
Nucleic Acid Atoms
Solvent Atoms	727
Heterogen Atoms	138

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.