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NMR-guided design of potent and selective EphA4 agonistic ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.10 M Na Acet, pH 4.50, 1.20 M K2HPO4, 0.80 M NaH2PO4
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.032 α = 90 b = 55.032 β = 90 c = 147.313 γ = 90
Symmetry Space Group P 43 21 2
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 2017-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0332 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.43 51.552 93.8 0.053 0.053 0.055 0.015 1 24.9 12.9 34710
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.544 57.1 0.883 0.883 1.012 0.48 0.534 1.2 4
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 5JR2 1.43 51.547 34710 1715 81.002 0.152 0.149 0.2065 0.2028 20.129
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] -0.066 -0.066 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 35.574 r_dihedral_angle_2_deg 30.957 r_dihedral_angle_other_6_deg 16.29 r_dihedral_angle_4_deg 14.844 r_dihedral_angle_6_deg 14.682 r_dihedral_angle_3_deg 11.43 r_dihedral_angle_1_deg 7.087 r_lrange_it 4.434 r_lrange_other 4.043 r_scangle_it 3.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 35.574 r_dihedral_angle_2_deg 30.957 r_dihedral_angle_other_6_deg 16.29 r_dihedral_angle_4_deg 14.844 r_dihedral_angle_6_deg 14.682 r_dihedral_angle_3_deg 11.43 r_dihedral_angle_1_deg 7.087 r_lrange_it 4.434 r_lrange_other 4.043 r_scangle_it 3.898 r_scangle_other 3.897 r_scbond_it 3.555 r_scbond_other 3.554 r_mcangle_it 3.195 r_mcangle_other 3.193 r_mcbond_it 2.948 r_mcbond_other 2.888 r_rigid_bond_restr 2.283 r_dihedral_angle_other_2_deg 1.592 r_angle_refined_deg 1.562 r_angle_other_deg 1.461 r_symmetry_nbd_other 0.177 r_nbd_refined 0.173 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.154 r_nbd_other 0.129 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.071 r_symmetry_nbd_refined 0.06 r_bond_refined_d 0.009 r_bond_other_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1558 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing