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Crystal structure of a chimeric MR78-like antibody chimera-1 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 287 4.5 M NaCl, 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 5 75.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.78 α = 90 b = 133.78 β = 90 c = 91.91 γ = 120
Symmetry Space Group P 31 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 300 mm CCD 2018-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.48 57.93 99.2 0.342 0.084 8.8 16.6 12393 145.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.48 3.54 98.7 4.159 0.995 1.1 17.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5JRP 3.48 57.93 11852 524 99.01 0.2961 0.2946 0.3059 0.3273 0.3278 RANDOM 172.603
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] 6.54 3.27 6.54 -21.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.546 r_mcangle_it 19.239 r_mcbond_other 14.163 r_mcbond_it 14.156 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_3_deg 7.527 r_dihedral_angle_1_deg 4.18 r_angle_other_deg 2.433 r_angle_refined_deg 2.178 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.546 r_mcangle_it 19.239 r_mcbond_other 14.163 r_mcbond_it 14.156 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_3_deg 7.527 r_dihedral_angle_1_deg 4.18 r_angle_other_deg 2.433 r_angle_refined_deg 2.178 r_chiral_restr 0.115 r_bond_other_d 0.036 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3259 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing PDB_EXTRACT data extraction xia2 data reduction PHENIX refinement