5SYJ

Crystal structure of the D141A variant of B. pseudomallei KatGin complex with isoniazid

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		293	16-20% PEG 4000, 20% MPD, 0.1 M sodium citrate pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.64	α = 90
b = 114.64	β = 90
c = 174.99	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	PIXEL	PSI PILATUS 6M		2013-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97949	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.88	95.89	98.4	0.063	14.3	3.6		155033

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	1.88	1.97	87.8		0.5623	1.57	2.91	7897

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MWV	1.88	20	155033	8160	98.42	0.1418	0.1403	0.1703	RANDOM	28.742

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]
-0.01			0.22		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.778
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	13.077
r_dihedral_angle_1_deg	6.074
r_mcangle_it	3.018
r_angle_refined_deg	2.296
r_mcbond_it	2.234
r_mcbond_other	2.231
r_angle_other_deg	1.337
r_chiral_restr	0.161

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.778
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	13.077
r_dihedral_angle_1_deg	6.074
r_mcangle_it	3.018
r_angle_refined_deg	2.296
r_mcbond_it	2.234
r_mcbond_other	2.231
r_angle_other_deg	1.337
r_chiral_restr	0.161
r_bond_refined_d	0.029
r_gen_planes_refined	0.016
r_gen_planes_other	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11004
Nucleic Acid Atoms
Solvent Atoms	1159
Heterogen Atoms	204

Software

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