2PZI

Crystal Structure of Protein kinase PknG from Mycobacterium tuberculosis in Complex with Tetrahydrobenzothiophene AX20017

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	293	0.1M Sodium Citrate, 0.2M Sodium Chloride, 1M Ammonium phosphate, 0.01M Cadmium Chloride , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.553	α = 90
b = 122.553	β = 90
c = 243.749	γ = 120

Symmetry
Space Group	P 65

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 225 mm CCD	mirrors	2006-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.008503	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	106	99.9			80540	80540		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.42	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	2.4	106	76493	76493	4045	99.91	0.18555	0.18555	0.1831	0.23339	RANDOM	47.621

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]
-0.13	-0.07		-0.13		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.651
r_dihedral_angle_4_deg	17.766
r_dihedral_angle_3_deg	16.866
r_scangle_it	7.726
r_scbond_it	5.787
r_dihedral_angle_1_deg	5.771
r_mcangle_it	3.482
r_mcbond_it	2.191
r_angle_refined_deg	1.394
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.651
r_dihedral_angle_4_deg	17.766
r_dihedral_angle_3_deg	16.866
r_scangle_it	7.726
r_scbond_it	5.787
r_dihedral_angle_1_deg	5.771
r_mcangle_it	3.482
r_mcbond_it	2.191
r_angle_refined_deg	1.394
r_nbtor_refined	0.302
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9975
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
SHARP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.