5KQ6 | pdb_00005kq6

Crystal structure of the A359D variant of catalase-peroxidase from B. 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	6.1	293	MPD

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.577	α = 90
b = 115.791	β = 90
c = 174.726	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	1.62	96.52	97.7	0.044	0.049	0.022	20.8	4.7	251711	251711

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	1.62	1.71	96.3		0.52	1.5	4.2

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	1.62	47.8	238907	12728	97.55	0.1458	0.1445	0.1583	0.1704	0.1805	RANDOM	23.856

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]
-0.47			1.42		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.587
r_dihedral_angle_4_deg	16.655
r_dihedral_angle_3_deg	13.288
r_dihedral_angle_1_deg	5.925
r_mcangle_it	2.898
r_angle_refined_deg	2.66
r_mcbond_it	2.086
r_mcbond_other	2.083
r_angle_other_deg	1.272
r_chiral_restr	0.183

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.587
r_dihedral_angle_4_deg	16.655
r_dihedral_angle_3_deg	13.288
r_dihedral_angle_1_deg	5.925
r_mcangle_it	2.898
r_angle_refined_deg	2.66
r_mcbond_it	2.086
r_mcbond_other	2.083
r_angle_other_deg	1.272
r_chiral_restr	0.183
r_bond_refined_d	0.034
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	11020
Nucleic Acid Atoms
Solvent Atoms	1579
Heterogen Atoms	136

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 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.