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Crystal structure of the complete EphA2 ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8X PDB ENTRIES 3C8X, 2E7H, 1X5L experimental model PDB 2E7H PDB ENTRIES 3C8X, 2E7H, 1X5L experimental model PDB 1X5L PDB ENTRIES 3C8X, 2E7H, 1X5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1/3 V/V: PROTEIN, 1/3 V/V: 20 % POLYETHYLENE GLYCOL 6000, 1 M LICL, 0.1 M TRIS PH 8 1/3 V/V: 0.4 M NON-DETERGENT SULFOBETAINE 256
Crystal Properties Matthews coefficient Solvent content 3.04 59.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.92 α = 93.02 b = 44.65 β = 98.22 c = 93.42 γ = 112.12
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 MARRESEARCH 2008-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3 91 94.9 0.15 6.5 1.71 23406 1 53.68
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 3 3.1 82.1 0.43 1.6 1.22
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRIES 3C8X, 2E7H, 1X5L 3 45.917 1.98 12037 594 97.63 0.2388 0.2357 0.2362 0.2986 0.2899
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] -35.9506 9.8252 10.3279 -43.4632 -5.4903 -33.124
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.221 f_angle_d 0.697 f_chiral_restr 0.045 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3728 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement XDS data reduction MOSFLM data reduction XSCALE data scaling PHASER phasing