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Design of amyloidogenic peptide traps
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other In-House de novo designed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 0.1 M Tris pH 7.8, poly-gamma-glutamic acid, 15% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.73 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.54 α = 90 b = 64.54 β = 90 c = 112.618 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 X 16M 2022-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 55.89 99.49 0.118 0.033 0.996 12.97 13.6 12554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.962 0.261 0.99 2.87 14.5
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 2.3 55.89 11921 603 99.59 0.21463 0.21248 0.2211 0.25952 0.2716 RANDOM 68.055
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] 1.94 0.97 1.94 -6.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.596 r_dihedral_angle_4_deg 20.691 r_dihedral_angle_3_deg 18.753 r_long_range_B_refined 12.754 r_long_range_B_other 12.724 r_scangle_other 11.289 r_scbond_it 7.244 r_scbond_other 7.222 r_dihedral_angle_1_deg 6.674 r_mcangle_other 5.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.596 r_dihedral_angle_4_deg 20.691 r_dihedral_angle_3_deg 18.753 r_long_range_B_refined 12.754 r_long_range_B_other 12.724 r_scangle_other 11.289 r_scbond_it 7.244 r_scbond_other 7.222 r_dihedral_angle_1_deg 6.674 r_mcangle_other 5.365 r_mcangle_it 5.351 r_mcbond_it 3.996 r_mcbond_other 3.936 r_angle_refined_deg 1.628 r_angle_other_deg 1.293 r_chiral_restr 0.174 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1275 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction