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Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 15% w/v PEG 8000, 0.1M Sodium Citrate pH 4.0
Crystal Properties Matthews coefficient Solvent content 2.84 56.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.3 α = 90 b = 116.91 β = 90 c = 64.67 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 100 PIXEL DECTRIS PILATUS3 R CdTe 300K 2020-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X17B1 0.92009 NSLS X17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.47 56.59 100 0.152 0.163 0.06 0.997 10.4 7.3 29660
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.53 99.9 1.215 1.31 0.486 0.595 7.2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3RI1 2.47 50.01 28141 1471 99.94 0.202 0.2006 0.2015 0.2293 0.2303 RANDOM 52.7
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 -0.43 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.193 r_dihedral_angle_4_deg 20.322 r_dihedral_angle_3_deg 17.695 r_dihedral_angle_1_deg 6.976 r_angle_refined_deg 1.37 r_chiral_restr 0.101 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4665 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction