5KSF

Crystal structure of the D141A variant of the catalase-peroxidase from B. pseudomallei treated with acetate

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, 0.1 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.692	α = 90
b = 115.474	β = 90
c = 174.586	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	0.9795	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	1.75	96.313	99.6	0.062	0.069	0.03	14.7	4.9	203501	203501

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	1.75	1.84	99.9		0.481	1.6	5

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	1.75	48.375	193124	10207	99.38	0.1492	0.1478	0.1751	RANDOM	27.877

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]
-1.12			2.08		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.16
r_dihedral_angle_4_deg	15.775
r_dihedral_angle_3_deg	13.257
r_dihedral_angle_1_deg	6.044
r_mcangle_it	3.314
r_angle_refined_deg	2.438
r_mcbond_it	2.425
r_mcbond_other	2.418
r_angle_other_deg	1.332
r_chiral_restr	0.176

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.16
r_dihedral_angle_4_deg	15.775
r_dihedral_angle_3_deg	13.257
r_dihedral_angle_1_deg	6.044
r_mcangle_it	3.314
r_angle_refined_deg	2.438
r_mcbond_it	2.425
r_mcbond_other	2.418
r_angle_other_deg	1.332
r_chiral_restr	0.176
r_bond_refined_d	0.031
r_gen_planes_refined	0.017
r_gen_planes_other	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11004
Nucleic Acid Atoms
Solvent Atoms	1439
Heterogen Atoms	142

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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 R01GM157729.