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PDGFRA-G680R mutant kinase domain in complex with a 6,7-bis(2-methoxyethoxy)quinazoline-based compound (44)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 10% PEG3350, 200 mM KCl, 100 mM Tris pH 7.5;293.15 K (cryoprotectant: glycerol)
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.8 α = 90 b = 71.9 β = 90 c = 102.47 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 PIXEL DECTRIS EIGER X 4M 2024-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 46.93 99.5 0.999 12.04 13.8 26935 36.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 0.651
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 41.73 1.36 26927 1346 99.52 0.1871 0.1855 0.1856 0.2169 0.2172 45.75
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.6927 f_angle_d 0.8833 f_chiral_restr 0.0556 f_bond_d 0.0077 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2543 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing