3LQ8

Structure of the kinase domain of c-Met bound to XL880 (GSK1363089)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house c-Met complex

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29112% PEG 4000, 15% isopropanol, 25 mM MOPS, pH 6.5, 150 mM NaCl, 2 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.925α = 90
b = 43.017β = 91.61
c = 89.618γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2004-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.0235.271000.0470.04718.63.1192251922025.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.022.1399.90.2680.2683.832788

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTin house c-Met complex2.0235.27192111822898399.920.193680.190640.25164RANDOM25.868
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]
-0.58-0.251.04-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.933
r_dihedral_angle_4_deg21.086
r_dihedral_angle_3_deg12.878
r_dihedral_angle_1_deg6.447
r_scangle_it3.657
r_scbond_it2.587
r_angle_refined_deg2.361
r_mcangle_it1.922
r_mcbond_it1.199
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.933
r_dihedral_angle_4_deg21.086
r_dihedral_angle_3_deg12.878
r_dihedral_angle_1_deg6.447
r_scangle_it3.657
r_scbond_it2.587
r_angle_refined_deg2.361
r_mcangle_it1.922
r_mcbond_it1.199
r_nbtor_refined0.305
r_symmetry_hbond_refined0.282
r_nbd_refined0.203
r_xyhbond_nbd_refined0.187
r_symmetry_vdw_refined0.164
r_chiral_restr0.119
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2216
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms46

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling