5KSK | pdb_00005ksk

Crystal structure of the catalase-peroxidase from B. pseudomallei treated with acetate

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, 0.1 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.703	α = 90
b = 115.48	β = 90
c = 174.966	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	0.97949	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	1.69	115.48	99.4	0.07	0.081	0.04	10.8	3.7	225720	225720

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	1.69	1.78	99.8		0.484	1.6	3.7

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	1.69	48.388	214411	11161	99.16	0.1534	0.152	0.16	0.1796	0.19	RANDOM	25.904

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]
-1.09			1.84		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.408
r_dihedral_angle_4_deg	15.92
r_dihedral_angle_3_deg	13.439
r_dihedral_angle_1_deg	6.105
r_mcangle_it	2.982
r_angle_refined_deg	2.396
r_mcbond_it	2.152
r_mcbond_other	2.15
r_angle_other_deg	1.339
r_chiral_restr	0.167

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.408
r_dihedral_angle_4_deg	15.92
r_dihedral_angle_3_deg	13.439
r_dihedral_angle_1_deg	6.105
r_mcangle_it	2.982
r_angle_refined_deg	2.396
r_mcbond_it	2.152
r_mcbond_other	2.15
r_angle_other_deg	1.339
r_chiral_restr	0.167
r_bond_refined_d	0.03
r_gen_planes_refined	0.017
r_gen_planes_other	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11014
Nucleic Acid Atoms
Solvent Atoms	1608
Heterogen Atoms	134

Software

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