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Structure of NNQQNY from yeast prion Sup35 with cadmium acetate determined by MicroED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 273 1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M cadmium sulfate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.074 α = 90 b = 4.932 β = 104.29 c = 23.51 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 1 100 CMOS TVIPS F416 CMOS CAMERA 2016-02-03
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ELECTRON MICROSCOPE TECNAI F20 TEM 0.0251
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 90 84.5 0.18 5.1 4.6 2564
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 1.08 66 0.282 3.3 365
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-Free (Depositor) R-Free Selection Details Mean Isotropic B ELECTRON CRYSTALLOGRAPHY THROUGHOUT 1 22.79 2308 253 80.97 0.2223 0.2203 0.2415 RANDOM 6.444
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] 0.23 0.36 -0.29 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 60.278 r_dihedral_angle_3_deg 8.34 r_sphericity_free 6.512 r_dihedral_angle_1_deg 5.527 r_sphericity_bonded 4.945 r_angle_refined_deg 1.688 r_angle_other_deg 0.957 r_rigid_bond_restr 0.84 r_mcbond_it 0.502 r_mcangle_it 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 60.278 r_dihedral_angle_3_deg 8.34 r_sphericity_free 6.512 r_dihedral_angle_1_deg 5.527 r_sphericity_bonded 4.945 r_angle_refined_deg 1.688 r_angle_other_deg 0.957 r_rigid_bond_restr 0.84 r_mcbond_it 0.502 r_mcangle_it 0.233 r_mcbond_other 0.189 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 55 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction
Sample Prion fibril composed of a 6-residue segment of Sup35 and cadmium
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Plunged into liquid ethane (FEI VITROBOT MARK IV)
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details The density map was obtained using measured diffraction intensities and phases acquired from crystallographic direct methods program SHELXD. Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 22.074 Length b 4.932 Length c 4.932 Angle Alpha 90 Angle Beta 104.29 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target maximum likelihood Overall B Value 6.44 Fitting Procedure Details
Data Acquisition Detector Type TVIPS TEMCAM-F416 (4k x 4k) Electron Dose (electrons/Å**2) 0.01
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TECNAI F20 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode DIFFRACTION Specimen Holder Model GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EM-Menu 1 DIFFRACTION INDEXING Denzo 1.98.7 MODEL FITTING Coot 0.8.2 OTHER SHELXD 2013/2 MODEL REFINEMENT refmac5 5.8.0135 CRYSTALLOGRAPHY MERGING SCALEPACK 1.98.7 RECONSTRUCTION SHELXD 2013/2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE