7QZF

SFX structure of dye-type peroxidase DtpB D152A/N245A variant in the ferric state

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.5	291	6.2 mg/mL of protein in 20mM Sodium phosphate buffer, 150mM NaCl pH 7 mixed with 125 mM mM MgCl2, 125 mM HEPES pH 7.5, 18% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.95	α = 90
b = 121.83	β = 90
c = 199.5	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	301	CCD	MPCCD		2021-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.127	SACLA	BL2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	32.1	100	0.926	0.219	3.88	1040		108174

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24			0.509	1.088

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6YRJ	2.2	32.1	102375	5434	99.67	0.2206	0.2181	0.2688	RANDOM	32.316

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]
0.4			-1.4		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.715
r_dihedral_angle_4_deg	18.142
r_dihedral_angle_3_deg	15.214
r_dihedral_angle_1_deg	7.122
r_angle_refined_deg	1.898
r_angle_other_deg	1.388
r_chiral_restr	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.715
r_dihedral_angle_4_deg	18.142
r_dihedral_angle_3_deg	15.214
r_dihedral_angle_1_deg	7.122
r_angle_refined_deg	1.898
r_angle_other_deg	1.388
r_chiral_restr	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13889
Nucleic Acid Atoms
Solvent Atoms	687
Heterogen Atoms	259

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	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 R01GM133198.