5V53 | pdb_00005v53

Crystal structure of the D141A/Q233E/N240D variant of catalase-peroxidase from B. pseudomallei with acetate 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

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.842	α = 90
b = 115.825	β = 90
c = 174.775	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	0.98	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	1.7	46.23	96.1	0.061	0.07	0.034	11.7	3.9	214623	214623

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	1.7	1.79	98.7		0.538	0.538	0.624	0.31	1.4	3.8	32021

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MWV	1.7	46.23	203772	10697	95.64	0.1434	0.1419	0.1558	0.1722	0.1821	RANDOM	25.554

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]
-0.77			1.41		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.583
r_dihedral_angle_4_deg	16.995
r_dihedral_angle_3_deg	13.135
r_dihedral_angle_1_deg	5.964
r_angle_refined_deg	2.454
r_angle_other_deg	1.246
r_chiral_restr	0.181
r_bond_refined_d	0.031
r_gen_planes_refined	0.017
r_gen_planes_other	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.583
r_dihedral_angle_4_deg	16.995
r_dihedral_angle_3_deg	13.135
r_dihedral_angle_1_deg	5.964
r_angle_refined_deg	2.454
r_angle_other_deg	1.246
r_chiral_restr	0.181
r_bond_refined_d	0.031
r_gen_planes_refined	0.017
r_gen_planes_other	0.012
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11004
Nucleic Acid Atoms
Solvent Atoms	1465
Heterogen Atoms	144

Software

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