5EYC | pdb_00005eyc

Crystal structure of c-Met in complex with naphthyridinone inhibitor 5

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293	12% PEG 4000, 3% (v/v) ethanol, 6% (v/v) isopropanol, 40 mM beta-mercaptoethanol, 100 mM HEPES (pH 7.8)

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.073	α = 90
b = 43.267	β = 90
c = 158.02	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	Varimax HR	2011-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.8	50	82.4	0.034	24.5	2.9		22824		-3	28.99

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	1.8	1.86	37.7		0.325	3.686	2.2	1021

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	4XMO	1.8	41.74	21619	1183	82.48	0.1946	0.1917	0.1914	0.2472	0.2448	RANDOM	31.058

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]
-0.51			1.91		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.96
r_dihedral_angle_3_deg	12.997
r_dihedral_angle_4_deg	11.069
r_dihedral_angle_1_deg	5.18
r_angle_refined_deg	1.156
r_angle_other_deg	0.855
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2297
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	29

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
AMoRE	phasing