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Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214 in complex with epitope peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CEA for VH and SARAH domain experimental model PDB 7BSC for VL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M CHES pH 9.5, 20% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.143 α = 90 b = 62.793 β = 94.419 c = 78.122 γ = 90
Symmetry Space Group P 1 21 1
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 2021-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.75 47.58 98.6 0.052 0.998 10.95 3.86 70833 36.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 97.2 0.961 0.708 1.05 3.83
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 1.75 36.46 1.34 70773 3540 98.5 0.1977 0.1958 0.2334 0.2658 53.94
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 5.7049 f_angle_d 0.8811 f_chiral_restr 0.0561 f_plane_restr 0.0074 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5355 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing