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Structure of the EphA2 LBDCRD bound to FabS1C_C1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FL7 residues 25-325 experimental model PDB 8TRS chain A res 1-136 and chain G Residues 1-125 (Fv fragment) experimental model PDB 8TRS chain A res 138-239 and chain G Residues 12-232 (Fc fragment)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 20% PEG3350, 200 mM sodium iodide (PACT Premiere solution E3)
Crystal Properties Matthews coefficient Solvent content 3.31 62.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.933 α = 90 b = 110.558 β = 90 c = 263.443 γ = 90
Symmetry Space Group P 21 2 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 Mirrors 2022-04-05 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 2.99 131.72 99.6 0.121 0.132 0.05 0.999 12 6.7 44485 103.88
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 2.99 3.1 98.6 2.214 2.427 0.975 0.349 0.9 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entries 3FL7 & 8TRS 3.25 131.72 1.34 34771 1683 99.57 0.2197 0.217 0.217 0.272 0.272 123.87
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 16.5283 f_angle_d 1.1614 f_chiral_restr 0.0627 f_plane_restr 0.0133 f_bond_d 0.0101
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10669 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement PHENIX refinement X-Area data reduction Aimless data scaling PHASER phasing