☰ Navigation Tabs
Structure of GNNQQNY from yeast prion Sup35 in space group P212121 determined by MicroED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH 7 273 water
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.16 α = 90 b = 4.93 β = 90 c = 40.51 γ = 90
Symmetry Space Group P 21 21 21
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) 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 1.05 20.11 72.7 0.189 0.218 0.992 4.18 1836 -3 8.654
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 1.05 1.19 75.1 0.438 0.497 0.813 2.26
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 1.05 20.11 1653 184 72.75 0.1781 0.1772 0.1856 RANDOM 4.705
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] 0.4 -0.42 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 56.662 r_dihedral_angle_3_deg 8.289 r_dihedral_angle_1_deg 5.988 r_angle_refined_deg 1.592 r_mcangle_it 1.117 r_angle_other_deg 0.747 r_mcbond_it 0.71 r_mcbond_other 0.581 r_chiral_restr 0.113 r_bond_refined_d 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 56.662 r_dihedral_angle_3_deg 8.289 r_dihedral_angle_1_deg 5.988 r_angle_refined_deg 1.592 r_mcangle_it 1.117 r_angle_other_deg 0.747 r_mcbond_it 0.71 r_mcbond_other 0.581 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 59 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction
Sample Prion fibril composed of a 7-residue segment of Sup35
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 23.16 Length b 4.93 Length c 4.93 Angle Alpha 90 Angle Beta 90 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target maximum likelihood Overall B Value 4.7 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 XDS Oct 15, 2015 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