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crystal structure of the receptor tyrosine kinase Human HER2 (ERBB2) YVMA mutant kinase domain in complex with inhibitor compound 27
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 8% PEG 3350,
0.1M Tris pH8.5,
0.5M NaCl
Crystal Properties Matthews coefficient Solvent content 2.13 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.42 α = 90 b = 59.42 β = 90 c = 82.484 γ = 120
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 EIGER2 S 16M 2022-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
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 1.69 29.71 99.98 0.091 0.1008 0.03261 0.998 15.38 9.4 36435 22.36
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 1.69 1.75 0.78 0.7405 0.2548 0.829 8.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.69 29.71 1.99 36543 1779 99.99 0.1661 0.1645 0.2025 0.2153 26.67
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 17.0452 f_angle_d 1.3759 f_chiral_restr 0.0788 f_plane_restr 0.0117 f_bond_d 0.0103
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2469 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement DENZO data reduction STARANISO data scaling PHASER phasing