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Crystal Structure of the PSMalpha3 Peptide Mutant L15A Forming Cross-Alpha Amyloid-like Fibril
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Reservoir contained 0.1 M CAPS pH 10.5, 40% v/v 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 1.68 26.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.41 α = 90 b = 10.67 β = 105.87 c = 29.6 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 R 4M 2016-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 17.47 96.3 0.137 0.171 0.987 4.09 2.68 2854 20.678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 95 0.559 0.692 0.851 1.56 2.652
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 5I55 1.5 17.47 2568 286 96.45 0.1995 0.1943 0.1982 0.2449 0.2433 RANDOM 18.714
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] 2.01 0.94 -0.3 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.488 r_dihedral_angle_3_deg 13.094 r_angle_other_deg 2.671 r_dihedral_angle_1_deg 2.581 r_angle_refined_deg 1.692 r_chiral_restr 0.096 r_bond_other_d 0.049 r_gen_planes_other 0.023 r_bond_refined_d 0.019 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 182 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction