9YMT | pdb_00009ymt

Staphylococcus aureus serine/threonine kinase Stk1 with inhibitor GW779439X

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	1 microlitre of 9 mg/mL Stk1 1-291, 5 mM MgCl2, 2% (w/v) benzamidine hydrochloride, 1 mM dithiothreitol, 20 mM HEPES pH 7.5, 150 mM NaCl and 2 mM GW779439X was mixed with 1 microlitre of reservoir solution: 80 mM 2-(N-morpholino)-ethanesulfonic acid, pH 6.0, 1.2 M sodium citrate, pH 7.0, 2% (w/v) benzamidine hydrochloride and 30 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.792	α = 90
b = 100.792	β = 90
c = 91.698	γ = 90

Symmetry
Space Group	P 43 21 2

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	DECTRIS PILATUS3 S 6M		2023-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.0	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.066	45.08	95.7	0.095	0.093	0.018	1	28.7	25.3		22007			42.62

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.066	2.235	80.3		2.01	2.059	0.436	0.643	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.07	45.08	1.34	22005	2000	74.52	0.2162	0.2128	0.2127	0.2495	0.2494	59.23

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.7207
f_angle_d	0.5337
f_chiral_restr	0.0429
f_plane_restr	0.005
f_bond_d	0.0016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2155
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	112

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing