3ZBX | pdb_00003zbx

X-ray Structure of c-Met kinase in complex with inhibitor 6-((6-(4- fluorophenyl)-(1,2,4)triazolo(4,3-b)(1,2,4)triazin-3-yl)methyl) quinoline.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WGJ	PDB ENTRY 2WGJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	286	C-MET COCRYSTALS WERE OBTAINED AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1.2 MICROLITERS OF PROTEIN SOLUTION (CONTAINING 7-13 MG/ML C-MET KD (RESIDUES 1051-1348) WITH A 5 FOLD MOLAR EXCESS OF C-MET INHIBITOR COMPOUND) WITH 1.2 MICROLITERS OF SOLUTION CONTAINING (0.05M CITRATE-PHOSPHATE PH 4.2, 200M NACL, AND 17.4% POLYETHYLENE GLYCOL MW=3350)

Crystal Properties
Matthews coefficient	Solvent content
2.41	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.857	α = 90
b = 94.127	β = 90
c = 46.418	γ = 90

Symmetry
Space Group	P 21 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	96	CCD	ADSC CCD		2005-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	50	84.9	0.07	13.1	2.8		15108			12.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	81.2		0.28	3.5	2.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2WGJ	2.2	47.06	14207	429	80.2	0.179	0.179	0.17	0.237	0.23	RANDOM	24.6

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]
-2.23			-7.89		10.13

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.6
c_scangle_it	3.14
c_scbond_it	2.23
c_mcangle_it	1.95
c_mcbond_it	1.26
c_angle_deg	0.8
c_improper_angle_d	0.59
c_bond_d	0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2256
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	27

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4	phasing