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Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8STG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M Sodium formate, 20% PEG3,3500+16% Glutaric acid, 0.16% Mellitic acid, 0.16% Oxalic acid, 0.16% Pimelic acid, 0.16% Sebacic acid,0.16% trans-Cinnamic acid, 0.02 M HEPES Na pH6.8
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.069 α = 90 b = 88.713 β = 90 c = 127.42 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 16M 2024-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.999990 SPring-8 BL45XU
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 3.25 47.67 89.9 0.981 5.2 5 10510
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 3.25 3.51 0.63
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.25 47.67 10481 560 88.943 0.283 0.2793 0.2828 0.3419 0.3396 87.518
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] -6.436 4.794 1.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.84 r_dihedral_angle_3_deg 11.807 r_dihedral_angle_6_deg 7.812 r_lrange_it 5.584 r_lrange_other 5.583 r_dihedral_angle_1_deg 5.314 r_mcangle_it 3.123 r_mcangle_other 3.123 r_scangle_it 2.677 r_scangle_other 2.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.84 r_dihedral_angle_3_deg 11.807 r_dihedral_angle_6_deg 7.812 r_lrange_it 5.584 r_lrange_other 5.583 r_dihedral_angle_1_deg 5.314 r_mcangle_it 3.123 r_mcangle_other 3.123 r_scangle_it 2.677 r_scangle_other 2.677 r_mcbond_it 1.744 r_mcbond_other 1.744 r_scbond_it 1.457 r_scbond_other 1.456 r_angle_refined_deg 0.869 r_symmetry_xyhbond_nbd_refined 0.403 r_angle_other_deg 0.337 r_dihedral_angle_other_3_deg 0.241 r_symmetry_nbd_refined 0.236 r_nbd_other 0.22 r_nbd_refined 0.213 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.133 r_dihedral_angle_other_2_deg 0.125 r_symmetry_nbtor_other 0.076 r_xyhbond_nbd_other 0.073 r_chiral_restr 0.042 r_symmetry_xyhbond_nbd_other 0.023 r_gen_planes_refined 0.004 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4372 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing