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Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with MRAL5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG3350, 10% ethylene glycol, 0.2M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 1.97 37.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.84 α = 90 b = 107.413 β = 109.04 c = 40.651 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 EIGER X 16M 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999990 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 28.43 96.5 0.999 15 6.7 227442
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.72
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NKA 1.6 38.46 32023 1763 96.38 0.16498 0.16312 0.177 0.1986 0.2117 RANDOM 21.313
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] -0.1 -0.19 1.09 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.083 r_dihedral_angle_2_deg 7.124 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 5.595 r_long_range_B_other 5.592 r_scangle_other 3.831 r_scbond_it 2.633 r_scbond_other 2.632 r_mcangle_it 2.491 r_mcangle_other 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.083 r_dihedral_angle_2_deg 7.124 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 5.595 r_long_range_B_other 5.592 r_scangle_other 3.831 r_scbond_it 2.633 r_scbond_other 2.632 r_mcangle_it 2.491 r_mcangle_other 2.49 r_mcbond_it 1.666 r_mcbond_other 1.666 r_angle_refined_deg 1.321 r_angle_other_deg 0.478 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2135 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing