5KSN

Crystal structure of the S324G variant of catalase-peroxidase from B. pseudomallei with INH bound

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, isoniazid

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.434	α = 90
b = 115.277	β = 90
c = 174.118	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)	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	1.87	96.12	98.9	0.084	13.5	3.6		164600

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	1.87	1.97	100		0.499	1.5	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	1.87	48.05	156292	8235	98.59	0.143	0.1415	0.1711	RANDOM	21.156

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]
-0.44			1.25		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.411
r_dihedral_angle_4_deg	17.013
r_dihedral_angle_3_deg	12.945
r_dihedral_angle_1_deg	5.928
r_mcangle_it	2.385
r_angle_refined_deg	2.166
r_mcbond_it	1.656
r_mcbond_other	1.654
r_angle_other_deg	1.158
r_chiral_restr	0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.411
r_dihedral_angle_4_deg	17.013
r_dihedral_angle_3_deg	12.945
r_dihedral_angle_1_deg	5.928
r_mcangle_it	2.385
r_angle_refined_deg	2.166
r_mcbond_it	1.656
r_mcbond_other	1.654
r_angle_other_deg	1.158
r_chiral_restr	0.154
r_bond_refined_d	0.027
r_gen_planes_refined	0.015
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	1607
Heterogen Atoms	160

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.