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Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5, 25% PEG 3,350, 3% 1,6-hexanediol
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.137 α = 90 b = 84.467 β = 93.87 c = 127.894 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 IMAGE PLATE RIGAKU RAXIS HTC 2015-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 1.75 28.92 99.3 0.042 0.999 17.9 3.6 78825 17.1
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 1.75 1.78 96.5 0.316 3.1 3.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4W4Z 1.75 28.92 74698 4103 99.21 0.17209 0.17036 0.1792 0.20416 0.2097 RANDOM 22.711
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] -0.13 -0.07 -0.04 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.31 r_dihedral_angle_4_deg 14.852 r_dihedral_angle_3_deg 12.03 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 6.151 r_long_range_B_other 6.151 r_scangle_other 2.805 r_mcangle_it 2.21 r_mcangle_other 2.21 r_scbond_it 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.31 r_dihedral_angle_4_deg 14.852 r_dihedral_angle_3_deg 12.03 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 6.151 r_long_range_B_other 6.151 r_scangle_other 2.805 r_mcangle_it 2.21 r_mcangle_other 2.21 r_scbond_it 1.779 r_scbond_other 1.779 r_angle_refined_deg 1.591 r_angle_other_deg 1.322 r_mcbond_other 1.321 r_mcbond_it 1.32 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6077 Nucleic Acid Atoms Solvent Atoms 685 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data scaling Aimless data scaling PHASER phasing Coot model building