☰ Navigation Tabs
Ligand recognition by A-class EPH receptors: crystal structures of the EPHA2 ligand-binding domain and the EPHA2/EPHRIN-A1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ETP PDB ENTRY 3ETP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG 4,000, 100 mM Tris, 100 mM Sodium Acetate, 3% ethylene glycol, pH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.271 α = 117.14 b = 91.187 β = 97.27 c = 91.132 γ = 100.79
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 315 2005-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.5 30 96.8 0.094 9.2 5.6 38120 36900
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 80.2 0.269 3.2 4.6
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 PDB ENTRY 3ETP 2.52 30 35046 1856 96.77 0.2362 0.23249 0.2421 0.3074 0.3192 RANDOM 2.64
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] -0.17 -0.71 1.79 0.03 -0.25 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_3_deg 16.822 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_1_deg 6.632 r_angle_refined_deg 1.492 r_scangle_it 0.459 r_scbond_it 0.401 r_mcangle_it 0.148 r_mcbond_it 0.09 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_3_deg 16.822 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_1_deg 6.632 r_angle_refined_deg 1.492 r_scangle_it 0.459 r_scbond_it 0.401 r_mcangle_it 0.148 r_mcbond_it 0.09 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8394 Nucleic Acid Atoms Solvent Atoms 1032 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction