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Crystal structure of the EphA2 S901E mutant intracellular KD-SAM domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PDO 4PDO, 3KKA experimental model PDB 3KKA 4PDO, 3KKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 287 0.2 M MgCl2, 0.1 M Bis-Tris pH5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.639 α = 90 b = 54.587 β = 95.223 c = 135.538 γ = 90
Symmetry Space Group I 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 287 IMAGE PLATE RIGAKU RAXIS HTC 2014-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.3 29.25 99.8 0.09 0.125 0.086 0.995 12 3.7 39708 31.98
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 2.3 2.38 0.656 0.905 0.621 0.643 1.8
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 4PDO, 3KKA 2.3 29.25 1.34 39703 2026 99.83 0.1903 0.1884 0.189 0.2257 0.2268 43.08
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 14.1874 f_angle_d 0.5199 f_chiral_restr 0.0417 f_plane_restr 0.0031 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5798 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 87
Software Software Software Name Purpose CrystalClear data collection XDS data reduction Aimless data scaling PHASER phasing Coot model building PHENIX refinement