6CAW

Crystal structure of the W95F variant of catalase-peroxidase from B. pseudomallei

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	MPD, 0.1 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.976	α = 90
b = 116.14	β = 90
c = 175.643	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	CCD	MARMOSAIC 300 mm CCD	mirrors	2016-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.98	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (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	1.95	96.88	96	0.077	0.09	0.046	10.8	3.5		143646

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.06	98.6		0.467	0.467	0.551	0.285	1.7	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDBID 1MWV	1.95	96.88	136094	7201	95.19	0.18	0.1781	0.2158	RANDOM	26.777

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]
-1.92			3.73		-1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.944
r_dihedral_angle_4_deg	17.71
r_dihedral_angle_3_deg	14.054
r_dihedral_angle_1_deg	6.396
r_angle_refined_deg	1.506
r_angle_other_deg	0.803
r_chiral_restr	0.101
r_gen_planes_refined	0.017
r_bond_refined_d	0.015
r_gen_planes_other	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.944
r_dihedral_angle_4_deg	17.71
r_dihedral_angle_3_deg	14.054
r_dihedral_angle_1_deg	6.396
r_angle_refined_deg	1.506
r_angle_other_deg	0.803
r_chiral_restr	0.101
r_gen_planes_refined	0.017
r_bond_refined_d	0.015
r_gen_planes_other	0.011
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11008
Nucleic Acid Atoms
Solvent Atoms	1301
Heterogen Atoms	126

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	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.