5KQ3

Crystal structure of the D141A/Q233E variant of catalase-peroxidase from B. pseudomallei

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MWV

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.044	α = 90
b = 114.028	β = 90
c = 174.505	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	2015-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97944	CLSI	08ID-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	1.85	47.728	89.3	0.076	0.088	0.042	9.8	3.7		152779

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	1.85	1.95	93.5		0.487	1.6	3.6

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	1MWV	1.85	47.728	145121	7576	88.85	0.1609	0.1592	0.195	RANDOM	28.639

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]
-0.67			1.64		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.979
r_dihedral_angle_4_deg	15.689
r_dihedral_angle_3_deg	13.32
r_dihedral_angle_1_deg	6.072
r_mcangle_it	2.804
r_angle_refined_deg	2.014
r_mcbond_it	1.939
r_mcbond_other	1.936
r_angle_other_deg	1.12
r_chiral_restr	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.979
r_dihedral_angle_4_deg	15.689
r_dihedral_angle_3_deg	13.32
r_dihedral_angle_1_deg	6.072
r_mcangle_it	2.804
r_angle_refined_deg	2.014
r_mcbond_it	1.939
r_mcbond_other	1.936
r_angle_other_deg	1.12
r_chiral_restr	0.136
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_gen_planes_other	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11008
Nucleic Acid Atoms
Solvent Atoms	1255
Heterogen Atoms	136

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
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.