7Q52 | pdb_00007q52

Crystal structure of S/T protein kinase PknG from Mycobacterium tuberculosis in complex with inhibitor L2W

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Y12

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	Mother Liquor: 0.2M CaCl2, 0.2 M TRIS, pH 8.5 and 20 % (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.327	α = 90
b = 37.016	β = 105.5
c = 106.781	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	196	PIXEL	DECTRIS EIGER2 X 16M		2021-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.35	51.5	98.4	0.999	1.67	6.8		12303			62.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	98.1		0.699		6.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4Y12	2.35	51.502	12246	627	98.377	0.218	0.215	0.21	0.2676	0.27	74.413

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]
3.035		1.561	1.17		-4.395

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.721
r_dihedral_angle_3_deg	15.893
r_lrange_it	12.976
r_dihedral_angle_4_deg	10.975
r_scangle_it	8.401
r_mcangle_it	7.626
r_dihedral_angle_1_deg	7.1
r_scbond_it	5.827
r_mcbond_it	5.161
r_angle_refined_deg	1.246
r_nbtor_refined	0.312
r_symmetry_xyhbond_nbd_refined	0.311
r_symmetry_nbd_refined	0.28
r_nbd_refined	0.227
r_metal_ion_refined	0.162
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.092
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2401
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing