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Structure of the EphA2 LBDCRD bound to FabS1CE_L1 in a 2:1 (EphA2 to Fab) ratio
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TV1 chain C, residues 27-328 experimental model PDB 8TV1 chain D, residues 1-136 and chain E residues 2-126 experimental model PDB 8TV1 chain D, residues 138-238 and chain E residues 128-232
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 16% PEG8000, 100 mM CHES 9.0, 200 mM Magnesium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.53 65.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.879 α = 90 b = 72.888 β = 89.04 c = 241.962 γ = 90
Symmetry Space Group C 1 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 mirrors 2022-09-26 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 4.5 120.96 99 0.142 0.168 0.089 0.997 9.4 3.5 9743 160
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 4.5 4.58 98.2 1.164 1.393 0.754 0.495 1 3.3
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 4.6 120.96 1.36 9106 911 98.8 0.2683 0.2651 0.2648 0.2982 0.2975 267.41
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 16.8788 f_angle_d 0.8991 f_chiral_restr 0.0502 f_plane_restr 0.0066 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7734 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing