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Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Islet Amyloid Polypeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 Formic acid
Crystal Properties Matthews coefficient Solvent content 1.54 15.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 4.864 α = 90 b = 20.466 β = 88.6 c = 20.855 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 PIXEL DECTRIS EIGER X 4M 2022-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.040 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.25 20.47 91.9 0.084 59.11 2 1063
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 1.25 1.27 94.8 0.155 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.25 20.47 1054 63 91.1 0.174 0.1772 0.201 0.1955 5.94
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] -0.115 0.189 -0.011 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.446 r_dihedral_angle_3_deg 14.912 r_dihedral_angle_1_deg 3.777 r_angle_refined_deg 1.733 r_angle_other_deg 1.045 r_mcangle_other 0.38 r_mcangle_it 0.376 r_mcbond_other 0.231 r_mcbond_it 0.23 r_scangle_it 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.446 r_dihedral_angle_3_deg 14.912 r_dihedral_angle_1_deg 3.777 r_angle_refined_deg 1.733 r_angle_other_deg 1.045 r_mcangle_other 0.38 r_mcangle_it 0.376 r_mcbond_other 0.231 r_mcbond_it 0.23 r_scangle_it 0.22 r_scangle_other 0.219 r_scbond_it 0.206 r_scbond_other 0.205 r_nbd_other 0.203 r_nbtor_refined 0.187 r_chiral_restr 0.043 r_xyhbond_nbd_refined 0.03 r_nbd_refined 0.014 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 51 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing Coot model building