5SXW

Crystal structure of the E198A variant of catalase-peroxidase KatG of Burkholderia pseudomallei

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		293	16-20% PEG 4000, 20% MPD, 25 mM NaCl, 0.1 M sodium citrate pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.34	α = 90
b = 116.02	β = 90
c = 174.71	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		2009-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	96.65	100	0.084	11.9	5.9		267341

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	1.6	1.69	100		0.55	2.8	5.5	38773

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	1.6	20	253932	13409	99.93	0.1443	0.143	0.1691	RANDOM	20.949

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]
-0.12			0.05		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.086
r_dihedral_angle_4_deg	15.739
r_dihedral_angle_3_deg	13.185
r_dihedral_angle_1_deg	5.82
r_angle_refined_deg	2.738
r_mcangle_it	2.711
r_mcbond_it	1.925
r_mcbond_other	1.92
r_angle_other_deg	1.491
r_chiral_restr	0.186

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.086
r_dihedral_angle_4_deg	15.739
r_dihedral_angle_3_deg	13.185
r_dihedral_angle_1_deg	5.82
r_angle_refined_deg	2.738
r_mcangle_it	2.711
r_mcbond_it	1.925
r_mcbond_other	1.92
r_angle_other_deg	1.491
r_chiral_restr	0.186
r_bond_refined_d	0.033
r_gen_planes_refined	0.018
r_gen_planes_other	0.012
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11011
Nucleic Acid Atoms
Solvent Atoms	1866
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	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.