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Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 7
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 Bis-Tris 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 1.92 35.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.57 α = 90 b = 106.22 β = 108.51 c = 40.27 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 PILATUS 2M 2020-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.47 38.19 99.6 0.014 1 9.79 6.74 44065 24.11
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 1.47 1.56 98.3 0.199 0.37 0.87 6.59
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 1.47 38.19 1.36 44052 2100 99.72 0.1669 0.1662 0.1662 0.18 0.1802 24.99
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 12.5851 f_angle_d 0.78 f_chiral_restr 0.0641 f_plane_restr 0.0105 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing