6CDQ | pdb_00006cdq

Crystal structure of the W202F variant of catalase-peroxidase from B. pseudomallei with INH bound.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MWV	PDBID 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
3.23	61.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.531	α = 90
b = 114.896	β = 90
c = 174.099	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	2017-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.98	CLSI	08B1-1

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	1.92	174.099	88.8	0.078	0.093	0.048	9.4	3.3	136130	136130

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	1.92	2.02	97.3		0.516	0.516	0.618	0.331	1.5	3.2

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	PDBID 1MWV	1.92	174.099	129234	6845	88.4	0.1676	0.1659	0.18	0.1989	0.21	RANDOM	26.538

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]
-0.59			1.62		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.544
r_dihedral_angle_4_deg	17.749
r_dihedral_angle_3_deg	14.022
r_dihedral_angle_1_deg	6.708
r_angle_refined_deg	1.399
r_angle_other_deg	0.764
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_gen_planes_other	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.544
r_dihedral_angle_4_deg	17.749
r_dihedral_angle_3_deg	14.022
r_dihedral_angle_1_deg	6.708
r_angle_refined_deg	1.399
r_angle_other_deg	0.764
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_gen_planes_other	0.009
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11004
Nucleic Acid Atoms
Solvent Atoms	1272
Heterogen Atoms	152

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.