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Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 14
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 7.6 291 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 Bicin pH 7.6, 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 1.93 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.56 α = 90 b = 107 β = 108.56 c = 40.36 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 1.12 38.26 94.4 0.093 1 11.5 6.97 94907 15.89
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 1.12 1.19 89.5 0.184 0.43 0.95 6.8
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 1.12 31.12 1.36 94901 2101 94.51 0.1641 0.1638 0.1632 0.1768 0.1763 20.03
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 12.6341 f_angle_d 1.1237 f_chiral_restr 0.0802 f_plane_restr 0.0155 f_bond_d 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2132 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing