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Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned heavy and light chain interfaces
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 20% PEG3,350, 0.04 M Citrate, 0.06 M BTP, pH6.4
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.761 α = 113.58 b = 79.597 β = 93.06 c = 85.983 γ = 102.3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.98 APS 21-ID-G
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 1.63 23.506 95.6 0.036 0.051 0.036 0.996 13.4 2 108557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.72 93.9 0.4 0.717 2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1FVE 1.63 23.506 1.97 108471 5444 95.58 0.1869 0.1854 0.1968 0.2153 0.2228 23.4495
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 13.114 f_angle_d 1.087 f_chiral_restr 0.042 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6499 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 18
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing