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Structure of FabS1CE3-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor (orthorhombic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other residues 1-126 and 1-127 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab experimental model Other residues 129-230 and 130-231 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M Ammonium Citrate dibasic, 20% PEG3350. This was set up as a Fab/EPOR complex, however no EPOR was observed upon solving the structure.
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.199 α = 90 b = 74.275 β = 90 c = 93.335 γ = 90
Symmetry Space Group P 21 21 21
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 1.96 74.28 99.9 0.073 0.079 0.031 0.999 18.5 6.5 37275 34.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.01 99.7 0.686 0.751 0.302 0.855 2.3 6
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 1.96 58.12 1.35 37210 1749 99.82 0.1893 0.1874 0.1869 0.2275 0.2277 42.12
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 15.8174 f_angle_d 0.9755 f_chiral_restr 0.062 f_plane_restr 0.0087 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3178 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing