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X-ray Structure of PHA-00665752 bound to the kinase domain of c-Met
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 4.6 286 CRYSTALS WERE OBTAINED AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD USING 1.2 MICROLITERS OF PROTEIN SOLUTION (CONTAINING 7-13 MG/ML C-MET KD PLUS A 5 FOLD MOLAR EXCESS OF PHA-00665752) AND 1.2 MICROLITERS OF MOTHER LIQUOR SOLUTION (0.05 M CITRATE-PHOSHPHATE 4.6, 0-0.275 M NACL, AND 21% W/V PEG 3350).
Crystal Properties Matthews coefficient Solvent content 2.42 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.435 α = 90 b = 95.787 β = 90 c = 45.601 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 85 CCD ADSC CCD 2006-09-20 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 2.1 50 95.8 0.07 37.2 3.6 19501 2 20.2
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 2.1 2.15 78 0.41 4 3.1
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WGJ 2.2 200 15892 770 89 0.2183 0.2183 0.2214 0.2754 RANDOM 43.1
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] 0.034 0.328 -0.363
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.1 c_scangle_it 2.99 c_mcangle_it 2.13 c_scbond_it 2.01 c_mcbond_it 1.31 c_angle_deg 0.9 c_improper_angle_d 0.6 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.1 c_scangle_it 2.99 c_mcangle_it 2.13 c_scbond_it 2.01 c_mcbond_it 1.31 c_angle_deg 0.9 c_improper_angle_d 0.6 c_bond_d 0.006 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 2284 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 43
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing