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Crystal structure of kinase domain of HER2 Exon 20 insertion mutant in complex with tucatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Bicine pH 8.5, 11% w/v
PEG 1500, 0.5mM Tucatinib
Crystal Properties Matthews coefficient Solvent content 1.72 28.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.412 α = 90 b = 81.699 β = 90 c = 94.936 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 298 PIXEL DECTRIS EIGER2 S 9M 2022-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979145 SSRF BL02U1
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 1.48 61.93 99.73 0.044 0.052 0.028 0.999 18.7 6.1 43125
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 1.48 1.518 0.999
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 (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 1.48 61.93 43125 2294 99.7 0.1469 0.1447 0.1521 0.187 0.1877 RANDOM 23.21
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] 0.27 0.26 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.499 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_1_deg 6.269 r_mcangle_it 1.784 r_mcbond_it 1.389 r_mcbond_other 1.371 r_angle_other_deg 1.304 r_angle_refined_deg 1.297 r_rigid_bond_restr 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.499 r_dihedral_angle_4_deg 14.744 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_1_deg 6.269 r_mcangle_it 1.784 r_mcbond_it 1.389 r_mcbond_other 1.371 r_angle_other_deg 1.304 r_angle_refined_deg 1.297 r_rigid_bond_restr 0.844 r_chiral_restr 0.07 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing