5KT9

Crystal structure of the catalase-peroxidase from B. pseudomallei treated with hydrogen peroxide and carbon monoxide

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
3.21	61.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.854	α = 90
b = 113.79	β = 90
c = 174.633	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	1.88	100.854	99.5	0.09	0.102	0.046	10.7	4.4	162264	162264

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	1.88	1.98	99.7		0.57	1.3	4.6

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	1.88	50	153938	8079	99.21	0.1786	0.1768	0.213	RANDOM	28.029

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]
-2.32			4.02		-1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.639
r_dihedral_angle_4_deg	16.861
r_dihedral_angle_3_deg	13.663
r_dihedral_angle_1_deg	6.152
r_mcangle_it	2.989
r_angle_refined_deg	2.241
r_mcbond_it	2.053
r_mcbond_other	2.047
r_angle_other_deg	1.269
r_chiral_restr	0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.639
r_dihedral_angle_4_deg	16.861
r_dihedral_angle_3_deg	13.663
r_dihedral_angle_1_deg	6.152
r_mcangle_it	2.989
r_angle_refined_deg	2.241
r_mcbond_it	2.053
r_mcbond_other	2.047
r_angle_other_deg	1.269
r_chiral_restr	0.157
r_bond_refined_d	0.028
r_gen_planes_refined	0.015
r_gen_planes_other	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11014
Nucleic Acid Atoms
Solvent Atoms	1415
Heterogen Atoms	134

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 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.