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Crystal structure of EphA7 mutant D751H
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 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.24 α = 90 b = 51.24 β = 90 c = 215.271 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 2021-01-20 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 3.05 71.76 92.5 0.185 0.988 11.2 1 5689
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 3.05 3.22 0.988
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 3.05 44.375 5376 255 92.524 0.201 0.1994 0.2103 0.247 0.2513 27.178
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] 0.526 0.263 0.526 -1.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.784 r_dihedral_angle_4_deg 20.486 r_dihedral_angle_3_deg 18.363 r_dihedral_angle_1_deg 8.584 r_lrange_it 2.266 r_lrange_other 2.265 r_angle_refined_deg 1.68 r_angle_other_deg 1.199 r_mcangle_it 0.691 r_mcangle_other 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.784 r_dihedral_angle_4_deg 20.486 r_dihedral_angle_3_deg 18.363 r_dihedral_angle_1_deg 8.584 r_lrange_it 2.266 r_lrange_other 2.265 r_angle_refined_deg 1.68 r_angle_other_deg 1.199 r_mcangle_it 0.691 r_mcangle_other 0.69 r_mcbond_it 0.358 r_mcbond_other 0.358 r_symmetry_xyhbond_nbd_refined 0.273 r_scangle_it 0.252 r_scangle_other 0.252 r_nbd_refined 0.23 r_nbd_other 0.209 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.134 r_symmetry_nbtor_other 0.079 r_scbond_it 0.071 r_scbond_other 0.071 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2212 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing