6CFQ | pdb_00006cfq

Crystal structure of the D141N variant of catalase-peroxidase from B. pseudomallei with INH bound

X-RAY DIFFRACTION

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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	20% MPD, 0.1 M sodium citrate, 17% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.641	α = 90
b = 115.506	β = 90
c = 174.546	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	2016-07-15	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	1.72	96.325	99.9	0.055	0.061	0.027	19.9	5	215015	215015

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	1.72	1.81	99.8		0.575	0.575	0.642	0.282	1.4	5

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	1.72	96.32	203924	10978	99.84	0.1429	0.1414	0.1552	0.1704	0.1809	RANDOM	24.132

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]
-0.78			1.57		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.579
r_dihedral_angle_4_deg	16.175
r_dihedral_angle_3_deg	12.762
r_dihedral_angle_1_deg	6.153
r_angle_refined_deg	1.497
r_angle_other_deg	0.794
r_chiral_restr	0.117
r_bond_refined_d	0.017
r_gen_planes_refined	0.016
r_gen_planes_other	0.011
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11010
Nucleic Acid Atoms
Solvent Atoms	1594
Heterogen Atoms	150

Software

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