☰ Navigation Tabs
The Crystal Structure of EphA2 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Sodium Acetate, 0.1M Sodium Cacodylate HCl pH6.5, 18% PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.98 37.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.931 α = 90 b = 107.504 β = 108.686 c = 40.691 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 6M 2023-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 38.576 97.8 0.087 11.7 5.3 37926
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 0.844
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 38.576 37891 1935 97.69 0.165 0.1641 0.1785 0.1903 0.203 17.476
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] -0.541 -0.257 1.073 -0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.154 r_dihedral_angle_6_deg 15.769 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 5.934 r_lrange_it 5.092 r_lrange_other 4.809 r_scangle_it 2.819 r_scangle_other 2.819 r_mcangle_it 1.941 r_mcangle_other 1.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.154 r_dihedral_angle_6_deg 15.769 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 5.934 r_lrange_it 5.092 r_lrange_other 4.809 r_scangle_it 2.819 r_scangle_other 2.819 r_mcangle_it 1.941 r_mcangle_other 1.941 r_scbond_it 1.684 r_scbond_other 1.683 r_mcbond_it 1.141 r_mcbond_other 1.136 r_angle_refined_deg 1.114 r_angle_other_deg 0.405 r_symmetry_nbd_refined 0.215 r_nbd_refined 0.206 r_nbd_other 0.186 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.164 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.059 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2136 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing