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Structure of FabS1CE1-EPR1-1 in complex with the erythropoietin receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y5V chain C residues 9-120 experimental model PDB 4Y5V chain C residues 122-223 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model Other residues 1-126 and 1-127 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab experimental model Other residues 129-230 and 130-231 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab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 5 298 0.1 M MMT buffer pH 5.0, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 3.03 59.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.165 α = 90 b = 91.612 β = 90 c = 216.735 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 EIGER2 X 16M mirrors 2023-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 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 2.85 108.37 99.9 0.122 0.133 0.052 0.997 10.8 6.5 34880 79.05
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 2.85 2.99 100 1.043 1.126 0.423 0.787 1.9 7.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 84.38 1.35 33077 1584 99.8 0.2216 0.2191 0.2727 0.2631 79.64
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 18.6046 f_angle_d 1.2174 f_chiral_restr 0.0631 f_plane_restr 0.0163 f_bond_d 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7894 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing