5DG5

CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THE HEPATOCYTE GROWTH FACTOR RECEPTOR C-MET IN COMPLEX WITH ALTIRATINIB ANALOG DP-4157

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	Protein at 9.5mg/ml in 20 mM Tris pH 8.5, 100mM NaCl, 14mM 2-mercaptoethanol with 5-molar excess of compound; crystallization condition: 1.0M diammonium hydrogen phosphate, 0.2M sodium chloride, 0.1M citrate pH 5.0 and 7.5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.69	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.13	α = 90
b = 115.88	β = 92.92
c = 90.16	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	CCD	ADSC QUANTUM 315r		2009-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9999	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.6	20	98.3	0.1	0.12	11.36	3.2		23076		-3	47.861

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.78	99.3		0.689	0.827	1.97	3.2

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	PDB entry 2g15	2.6	19.65	21913	1161	98.25	0.2057	0.2036	0.2449	RANDOM	43.412

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]
-1.37		-0.51	-3.3		4.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.051
r_dihedral_angle_4_deg	19.521
r_dihedral_angle_3_deg	16.758
r_dihedral_angle_1_deg	5.515
r_mcangle_it	3.823
r_mcbond_it	2.258
r_mcbond_other	2.255
r_angle_refined_deg	1.196
r_angle_other_deg	0.893
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.051
r_dihedral_angle_4_deg	19.521
r_dihedral_angle_3_deg	16.758
r_dihedral_angle_1_deg	5.515
r_mcangle_it	3.823
r_mcbond_it	2.258
r_mcbond_other	2.255
r_angle_refined_deg	1.196
r_angle_other_deg	0.893
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4603
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	74

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

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 R01GM133198.