3CD8

X-ray Structure of c-Met with triazolopyridazine Inhibitor.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RFN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.82980.1M HEPES pH 7.8, 15% PEG 4K, 6% 2-Propanol, 40mM BME, and 3% Ethanol, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0339.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.008α = 90
b = 43.208β = 90
c = 158.219γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130IMAGE PLATERIGAKU RAXIS IV++varimax optics2006-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
125094.30.056293.52042719263-1-1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0778.80.1936.22.31587

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2RFN250192181821597394.780.235870.235870.233280.28678RANDOM32.191
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]
-0.742.99-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.953
r_dihedral_angle_4_deg14.852
r_dihedral_angle_3_deg13.747
r_dihedral_angle_1_deg5.189
r_scangle_it1.444
r_angle_refined_deg1.105
r_scbond_it0.994
r_mcangle_it0.907
r_mcbond_it0.554
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.953
r_dihedral_angle_4_deg14.852
r_dihedral_angle_3_deg13.747
r_dihedral_angle_1_deg5.189
r_scangle_it1.444
r_angle_refined_deg1.105
r_scbond_it0.994
r_mcangle_it0.907
r_mcbond_it0.554
r_nbtor_refined0.301
r_nbd_refined0.176
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.109
r_symmetry_vdw_refined0.105
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2189
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing