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Structure of the EphA2 LBDCRD bound to FabS1C_L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TRV chain A residues 27-201 experimental model PDB 8TRV chain A residues 203-328 experimental model PDB 8TRV chain D residues 1-136 and chain E residues 1-126 experimental model PDB 8TRV chain D residues 138-238 and chain E residues 128-232
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 14% PEG 20K, 100 mm HEPES 7.0, 200 mM KSCN
Crystal Properties Matthews coefficient Solvent content 3.12 60.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.437 α = 90 b = 73.249 β = 107.43 c = 118.57 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 2022-11-04 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 2.6 62.2 91.4 0.13 0.149 0.072 0.989 6.2 3.9 28513 54.37
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 2.6 2.72 79.4 1.102 1.269 0.619 0.612 1.7 3.8
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 2.6 62.2 1.34 28500 1992 91.05 0.2048 0.2016 0.2035 0.2462 0.2474 66.12
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 17.793 f_angle_d 1.0405 f_chiral_restr 0.0557 f_plane_restr 0.0089 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5542 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing