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Crystal Structure of Chimeric Antibody C2H7 Fab in complex with a CD20 Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSL PDB ENTRY 2OSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 277 0.2M di-ammonium hydrogen phosphate, 20% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.49 α = 90 b = 96.49 β = 90 c = 107.613 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 4 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
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 2.6 20 97.6 0.1 0.1 8.5 11.4 16029 15644 61.2
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 2.6 2.69 98.7 0.488 0.488 4.5 10.9 1538
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT PDB ENTRY 2OSL 2.61 20 15976 15609 781 97.7 0.237 0.234 0.2433 0.301 0.2437 RANDOM 25.13
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] -0.93 -0.93 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_3_deg 19.236 r_dihedral_angle_4_deg 16.546 r_dihedral_angle_1_deg 6.495 r_angle_refined_deg 1.22 r_scangle_it 1.179 r_scbond_it 0.726 r_mcangle_it 0.595 r_mcbond_it 0.348 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_3_deg 19.236 r_dihedral_angle_4_deg 16.546 r_dihedral_angle_1_deg 6.495 r_angle_refined_deg 1.22 r_scangle_it 1.179 r_scbond_it 0.726 r_mcangle_it 0.595 r_mcbond_it 0.348 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.268 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3456 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling