5KT8

Crystal structure of the W139F variant of the catalase-peroxidase from B. pseudomallei treated with isoniazid

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, isoniazid

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.651	α = 90
b = 112.782	β = 90
c = 174.539	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	2	174.539	94.5	0.079	0.09	0.042	14.6	4	126470	126470

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	96.5		0.546	0.546	0.627	0.3	1.4	3.9	18696

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	2	48.356	120133	6269	94.03	0.152	0.1502	0.1863	RANDOM	31.46

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]
-0.81			2.1		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.453
r_dihedral_angle_4_deg	15.371
r_dihedral_angle_3_deg	13.897
r_dihedral_angle_1_deg	5.953
r_mcangle_it	2.994
r_mcbond_it	2.071
r_mcbond_other	2.07
r_angle_refined_deg	2.041
r_angle_other_deg	1.185
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.453
r_dihedral_angle_4_deg	15.371
r_dihedral_angle_3_deg	13.897
r_dihedral_angle_1_deg	5.953
r_mcangle_it	2.994
r_mcbond_it	2.071
r_mcbond_other	2.07
r_angle_refined_deg	2.041
r_angle_other_deg	1.185
r_chiral_restr	0.132
r_bond_refined_d	0.024
r_gen_planes_refined	0.013
r_gen_planes_other	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11008
Nucleic Acid Atoms
Solvent Atoms	1186
Heterogen Atoms	160

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
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.