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Structure of FabS1CE1-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VUI residues 1-126 and 1-127 (IMGT numbering) of Fab heavy chain and light chain, respectively, of D_1000281027 experimental model PDB 8VUI residues 129-230 and 130-231 (IMGT numbering) of Fab heavy chain and light chain, respectively, of D_1000281027
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1 M HEPES 7.0, 30% Jeffamine ED-2003
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.933 α = 90 b = 72.933 β = 90 c = 153.366 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 PIXEL DECTRIS EIGER X 16M 2023-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 3.13 153.37 99.9 0.074 0.078 0.025 1 19.5 9.8 8839 139.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.13 3.35 100 2.017 2.121 0.651 0.505 1.2 10.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.27 58.4 1.35 7741 403 99.87 0.2472 0.2454 0.2453 0.2823 0.2822 143.82
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 5.0143 f_angle_d 0.6094 f_chiral_restr 0.0432 f_plane_restr 0.0125 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3137 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing