5KQN

Crystal structure of the H381S 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
3.25	62.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.986	α = 90
b = 114.174	β = 90
c = 175.544	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	1.75	46.179	94.3	0.062	0.069	0.03	14.1	4.7	191652	191652

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	97.1		0.551	1.4	4.7

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	46.179	182041	9473	93.88	0.1543	0.1528	0.1824	RANDOM	27.629

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]
-1.37			1.92		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.433
r_dihedral_angle_4_deg	15.934
r_dihedral_angle_3_deg	13.609
r_dihedral_angle_1_deg	6.206
r_mcangle_it	2.933
r_angle_refined_deg	2.349
r_mcbond_it	2.222
r_mcbond_other	2.221
r_angle_other_deg	1.212
r_chiral_restr	0.165

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.433
r_dihedral_angle_4_deg	15.934
r_dihedral_angle_3_deg	13.609
r_dihedral_angle_1_deg	6.206
r_mcangle_it	2.933
r_angle_refined_deg	2.349
r_mcbond_it	2.222
r_mcbond_other	2.221
r_angle_other_deg	1.212
r_chiral_restr	0.165
r_bond_refined_d	0.03
r_gen_planes_refined	0.017
r_gen_planes_other	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11006
Nucleic Acid Atoms
Solvent Atoms	1447
Heterogen Atoms	124

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 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.