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Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for the type I / type II distinction of anti- CD20 antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5, 24% (w/v) PEG4000, 0.15 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 273.14 α = 90 b = 38.038 β = 98.89 c = 90.22 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 225 mm CCD 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.5 50 97.6 0.105 0.067 12.42 3.3 32252 31465 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.66 93.1 0.418 0.277 3.6 2.8
Refinement Statistics Diffraction ID Structure Solution 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 1T04 2.508 25 1.99 31432 1998 97.56 0.21 0.2059 0.1987 0.2693 0.2623 RANDOM
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] -7.1872 2.2572 2.0538 5.1334
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.373 f_angle_d 0.668 f_chiral_restr 0.045 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6673 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms
Software Software Software Name Purpose Exes data collection PHASER phasing PHENIX refinement XDS data reduction XDS data scaling