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Crystal Structure of EphA2/SHIP2 Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KKA 3KKA and 2K4P experimental model PDB 2K4P 3KKA and 2K4P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 0.2M Succinic acid pH 7.0, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.283 α = 90 b = 43.344 β = 95.35 c = 46.377 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 CCD ADSC QUANTUM 315r 2014-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 50 99 0.047 0.056 0.029 14.9 3.6 43485
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 1.5 1.53 98.1 0.624 0.736 0.386 0.87 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KKA and 2K4P 1.5 50 41294 2188 98.79 0.1458 0.1434 0.1456 0.1911 0.1935 RANDOM 31.151
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] 0.18 -0.66 0.7 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.197 r_sphericity_free 29.589 r_dihedral_angle_4_deg 14.747 r_dihedral_angle_3_deg 13.456 r_sphericity_bonded 13.133 r_dihedral_angle_1_deg 4.549 r_rigid_bond_restr 1.395 r_angle_refined_deg 1.224 r_angle_other_deg 0.953 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.197 r_sphericity_free 29.589 r_dihedral_angle_4_deg 14.747 r_dihedral_angle_3_deg 13.456 r_sphericity_bonded 13.133 r_dihedral_angle_1_deg 4.549 r_rigid_bond_restr 1.395 r_angle_refined_deg 1.224 r_angle_other_deg 0.953 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2007 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing