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Crystal structure of EphA7 mutant G656E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2REI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295.15 PEG3350, Ammonium sulphate, HEPES
Crystal Properties Matthews coefficient Solvent content 2.37 48.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.36 α = 90 b = 51.36 β = 90 c = 215.172 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 53.79 99.9 0.12 0.997 15.9 1 9920
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 2.6 2.74 0.927
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2REI 2.6 44.479 9853 541 99.899 0.246 0.244 0.2797 0.2337 26.474
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] -0.208 -0.104 -0.208 0.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.573 r_dihedral_angle_4_deg 23.196 r_dihedral_angle_3_deg 18.018 r_dihedral_angle_1_deg 8.209 r_angle_refined_deg 1.621 r_angle_other_deg 1.189 r_symmetry_xyhbond_nbd_other 0.426 r_symmetry_nbd_refined 0.227 r_nbd_refined 0.226 r_nbd_other 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.573 r_dihedral_angle_4_deg 23.196 r_dihedral_angle_3_deg 18.018 r_dihedral_angle_1_deg 8.209 r_angle_refined_deg 1.621 r_angle_other_deg 1.189 r_symmetry_xyhbond_nbd_other 0.426 r_symmetry_nbd_refined 0.227 r_nbd_refined 0.226 r_nbd_other 0.217 r_lrange_it 0.212 r_xyhbond_nbd_refined 0.21 r_lrange_other 0.209 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.163 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.069 r_mcangle_it 0.042 r_mcangle_other 0.042 r_mcbond_it 0.022 r_mcbond_other 0.022 r_scangle_it 0.017 r_scangle_other 0.017 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_scbond_it 0.006 r_scbond_other 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing