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Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 37,5 % Precipitant Mix 4 (25% (v/v) Hexylene glycol, 25% (w/v) Poly(ethylene glycol) 1000, 25% (w/v) Poly(ethylene glycol) 3350),
0.1M Tris-HCl pH 6.5,
0.1 M Amino acids mix (0.2 M DL-Alanine,
0.2M DL-Glutamic acid monohydrate, 0.2M
DL-Lysine monohydrochloride, 0.2M
DL-Serine, 0.2M Glycine)
Crystal Properties Matthews coefficient Solvent content 1.94 36.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.7 α = 90 b = 106.58 β = 108.52 c = 40.39 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 6M 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.42 38.3 98.7 0.011 1 11.52 6.8 49017 23.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.5 96.4 0.174 0.48 1.08 6.57
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 6q7d 1.42 38.3 1.36 49012 2099 98.82 0.1587 0.158 0.1579 0.1742 0.1746 22.79
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 12.8312 f_angle_d 1.137 f_chiral_restr 0.0877 f_plane_restr 0.016 f_bond_d 0.0117
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2151 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction d*TREK data scaling PHASER phasing