9T08 | pdb_00009t08

Crystal structure of wild-type c-MET bound by sitravatinib.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Non-public model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG4K, 10% isopropanol, 0.1 M Na-HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.57	α = 90
b = 42.434	β = 90.72
c = 89.884	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER2 X 16M		2024-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

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	1.46	44.94	86.7	0.998	7.8	3.2		25802

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	1.46	1.64			0.698

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.462	44.94	25802	1338	51	0.2138	0.2122	0.2066	0.2425	0.2385	RANDOM	26.02

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]
0.7355		0.431	-0.3272		-0.4082

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.96
t_omega_torsion	3.4
t_angle_deg	0.97
t_bond_d	0.011
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2065
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	45

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing