5KQH

Crystal structure of the V293D 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
3.2	61.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.787	α = 90
b = 113.434	β = 90
c = 174.677	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	1.82	47.561	99.9	0.071	0.081	0.038	14.2	4.3	178897	178897

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	1.82	1.92	100		0.475	1.6	4.4

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		THROUGHOUT	1MWV	1.82	47.561	169937	8889	99.79	0.1559	0.1544	0.1839	RANDOM	22.762

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]
-0.57			1.31		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.822
r_dihedral_angle_4_deg	16.218
r_dihedral_angle_3_deg	14.092
r_dihedral_angle_1_deg	6.033
r_mcangle_it	2.519
r_angle_refined_deg	2.264
r_mcbond_it	1.734
r_mcbond_other	1.728
r_angle_other_deg	1.195
r_chiral_restr	0.161

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.822
r_dihedral_angle_4_deg	16.218
r_dihedral_angle_3_deg	14.092
r_dihedral_angle_1_deg	6.033
r_mcangle_it	2.519
r_angle_refined_deg	2.264
r_mcbond_it	1.734
r_mcbond_other	1.728
r_angle_other_deg	1.195
r_chiral_restr	0.161
r_bond_refined_d	0.027
r_gen_planes_refined	0.016
r_gen_planes_other	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11016
Nucleic Acid Atoms
Solvent Atoms	1550
Heterogen Atoms	135

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.