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Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin 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model Other residues 1-126 and 1-127 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab experimental model Other residues 129-230 and 130-231 (IMGT numbering) of Fab heavy chain and light chain, respectively, of an unpublished Fab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 5.2 298 0.2 M Ammonium Citrate dibasic, 20% PEG2000 monomethyl ether, pH 5.2
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.39 α = 90 b = 71.93 β = 90 c = 197.02 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 2022-06-21 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 2.06 98.51 92.5 0.107 0.117 0.046 0.995 9.3 6.5 46837 39.21
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 2.06 2.12 69.7 1.193 1.298 0.506 0.723 1.9 6.6
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 2.1 98.51 1.34 44968 1927 94.12 0.1991 0.1973 0.1998 0.2398 0.2406 52.85
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 17.0999 f_angle_d 0.9434 f_chiral_restr 0.0578 f_plane_restr 0.0084 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4700 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing