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Amyloid Beta KLVFFAENVGS 16-26 D23N Iowa mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y2A PDB entry 2Y2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 UNSPECIFIED
Crystal Properties Matthews coefficient Solvent content 1.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 11.67 α = 90 b = 51.91 β = 114.18 c = 12.76 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 electron 2014-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ELECTRON MICROSCOPE 1.000
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 1.4 11.64 85.4 0.24 0.246 0.995 9.06 20.211 2355 7.23
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 1.4 1.44 78 0.652 0.682 0.697 2.88 12.061
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B ELECTRON CRYSTALLOGRAPHY MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2Y2A 1.402 11.64 1.52 2354 236 86.16 0.2419 0.2368 0.2832 9.4646
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.776 f_angle_d 1.458 f_chiral_restr 0.067 f_bond_d 0.014 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 178 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing
Sample Fibrils of Amyloid Beta segment 16-26
Specimen Preparation Sample Aggregation State 3D ARRAY Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method CRYSTALLOGRAPHY Number of Particles Reported Resolution (Å) 1.402 Resolution Method DIFFRACTION PATTERN/LAYERLINES Other Details Refinement Type Symmetry Type 3D CRYSTAL Space Group Name Length a 11.67 Length b 51.91 Length c 51.91 Angle Alpha 90 Angle Beta 114.18 Angle Gamma 90
Map-Model Fitting and Refinement Id 1 (2Y2A) Refinement Space RECIPROCAL Refinement Protocol OTHER Refinement Target Maximum likelihood Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TVIPS TEMCAM-F416 (4k x 4k) Electron Dose (electrons/Å**2) 0.03
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 MODEL FITTING Coot MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE