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Crystal structure of anti-MET Fab arm of amivantamab in complex with human MET
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHY 1SHY and 4LEO experimental model PDB 4LEO 1SHY and 4LEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 2.5M sodium formate, 5% PEG 400, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.96 68.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.83 α = 90 b = 86.83 β = 90 c = 457.099 γ = 90
Symmetry Space Group P 43 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 PILATUS 6M 2014-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.1 40.45 94.9 0.11 0.11 0.121 0.049 7.2 5.1 31529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.15 96.7 0.431 0.431 0.06 0.024 0.996 2.4 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1SHY and 4LEO 3.1 40.45 1.39 31392 1592 94.9 0.192 0.19 0.1969 0.235 0.2349 Random selection
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 10.041 f_angle_d 0.875 f_chiral_restr 0.057 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7054 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 149
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction