6O4J

Amyloid Beta KLVFFAENVGS 16-26 D23N Iowa mutation


ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y2APDB entry 2Y2A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1UNSPECIFIED
Crystal Properties
Matthews coefficientSolvent content
1.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 11.67α = 90
b = 51.91β = 114.18
c = 12.76γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11electron2014-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ELECTRON MICROSCOPE1.000

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.411.6485.40.240.2460.9959.0620.21123557.23
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)RedundancyNumber Unique Reflections (All)
11.41.44780.6520.6820.6972.8812.061

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
ELECTRON CRYSTALLOGRAPHYMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2Y2A1.40211.641.52235423686.160.24190.23680.28329.4646
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.776
f_angle_d1.458
f_chiral_restr0.067
f_bond_d0.014
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms178
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Sample
Fibrils of Amyloid Beta segment 16-26
Specimen Preparation
Sample Aggregation State3D ARRAY
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodCRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)1.402
Resolution MethodDIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type3D CRYSTAL
Space Group Name
Length a11.67
Length b51.91
Length c51.91
Angle Alpha90
Angle Beta114.18
Angle Gamma90
Map-Model Fitting and Refinement
Id1 (2Y2A)
Refinement SpaceRECIPROCAL
Refinement ProtocolOTHER
Refinement TargetMaximum likelihood
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeTVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å**2)0.03
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeDIFFRACTION
Specimen Holder ModelGATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONE