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Crystal structure of amyloidogenic peptide Bz-FFAALL-NH2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7N8R Polyalanine model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 Formic acid
Crystal Properties Matthews coefficient Solvent content 1.52 19.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 4.813 α = 90 b = 32.067 β = 99.24 c = 13.478 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 2023-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 32.07 99.2 0.052 0.062 0.033 0.999 25.6 6.3 2196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.05 97.9 0.063 0.078 0.045 0.995 5.3
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-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 1 16.03 2055 125 99.09 0.03653 0.03602 0.068 0.04439 0.0691 RANDOM 2.97
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] -0.41 0.49 0.07 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 9.52 r_dihedral_angle_3_deg 7.779 r_rigid_bond_restr 5.399 r_dihedral_angle_1_deg 4.421 r_angle_refined_deg 1.555 r_angle_other_deg 1.322 r_long_range_B_refined 0.641 r_long_range_B_other 0.636 r_scangle_other 0.559 r_mcbond_it 0.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 9.52 r_dihedral_angle_3_deg 7.779 r_rigid_bond_restr 5.399 r_dihedral_angle_1_deg 4.421 r_angle_refined_deg 1.555 r_angle_other_deg 1.322 r_long_range_B_refined 0.641 r_long_range_B_other 0.636 r_scangle_other 0.559 r_mcbond_it 0.506 r_mcangle_it 0.5 r_mcangle_other 0.497 r_mcbond_other 0.482 r_scbond_it 0.474 r_scbond_other 0.469 r_chiral_restr 0.063 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing Coot model building REFMAC refinement