☰ Navigation Tabs
Crystal structure of PTK6 Kinase Domain complexed with Dasatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M tri-Lithium citrate, 20 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.881 α = 81.36 b = 77.018 β = 75.76 c = 87.413 γ = 74.92
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 MAR scanner 345 mm plate VariMax HR 2015-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54789
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 2.24 84.52 94.7 0.099 9.3 2.4 58073
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 2.24 2.32 83.1 0.487 1.5 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5D7V 2.24 84.52 52220 2789 94.46 0.2083 0.2055 0.2601 0.2516 RANDOM 33.687
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] 0.85 -0.52 0.96 0.23 -0.05 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.871 r_dihedral_angle_3_deg 17.93 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_1_deg 5.844 r_scangle_it 1.913 r_angle_refined_deg 1.31 r_scbond_it 1.212 r_mcangle_it 0.834 r_mcbond_it 0.49 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.871 r_dihedral_angle_3_deg 17.93 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_1_deg 5.844 r_scangle_it 1.913 r_angle_refined_deg 1.31 r_scbond_it 1.212 r_mcangle_it 0.834 r_mcbond_it 0.49 r_nbtor_refined 0.299 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8541 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing HKL data scaling