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EphA2 LBD in complex with bA-WLA-YRPKbio peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.09 M Sodium-Acetate pH 4.5, 22.5% w/v PEG 3,350, 3% w/v 6-aminohexanoic acid
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.684 α = 99.391 b = 48.137 β = 96.791 c = 50.211 γ = 90.197
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2018-10-01 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 1.55 27.6 87.9 0.021 0.03 0.021 0.999 12.3 2 52329 15.91
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 1.55 1.58 83.4 0.108 0.152 0.108 0.976 4.4 2
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 6NJZ 1.55 27.6 2.03 52324 2722 87.96 0.1469 0.1457 0.1468 0.1686 0.1692 24.67
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 10.0253 f_angle_d 1.0307 f_chiral_restr 0.0612 f_bond_d 0.0084 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3098 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction