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Crystal structure of EphA7 mutant G656R
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 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.78 α = 90 b = 51.78 β = 90 c = 216.08 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 3.1 72.03 100 0.175 0.984 11.9 1 5944
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 3.1 3.27 0.175
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2REI 3.1 44.8428 5944 294 100 0.183 0.1813 0.1844 0.2101 0.2157 32.018
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] 0.056 0.028 0.056 -0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.463 r_dihedral_angle_3_deg 16.956 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_1_deg 7.887 r_angle_refined_deg 1.589 r_angle_other_deg 1.209 r_lrange_it 0.901 r_lrange_other 0.901 r_symmetry_xyhbond_nbd_refined 0.322 r_nbd_refined 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.463 r_dihedral_angle_3_deg 16.956 r_dihedral_angle_4_deg 15.355 r_dihedral_angle_1_deg 7.887 r_angle_refined_deg 1.589 r_angle_other_deg 1.209 r_lrange_it 0.901 r_lrange_other 0.901 r_symmetry_xyhbond_nbd_refined 0.322 r_nbd_refined 0.225 r_nbd_other 0.219 r_symmetry_nbd_other 0.2 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.162 r_mcangle_it 0.157 r_mcangle_other 0.157 r_symmetry_xyhbond_nbd_other 0.09 r_mcbond_it 0.081 r_mcbond_other 0.081 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.062 r_scangle_it 0.054 r_scangle_other 0.054 r_xyhbond_nbd_other 0.015 r_scbond_it 0.012 r_scbond_other 0.012 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2211 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing