Experiment: 6NB9

ELECTRON CRYSTALLOGRAPHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH	7.6	310	0.05M Tris-HCl, 0.15M NaCl, 1% DMSO

Crystal Properties
Matthews coefficient	Solvent content
1.51	18.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.2	α = 90
b = 4.87	β = 101.9
c = 32.44	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 CAMERA	CETA 16M		2018-04-13

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	TALOS ARCTICA	0.0251

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	5.955	82.7	0.197	0.224	0.984	3.76	4.189		3946			9.691

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	1.1	53		0.494	0.589	0.779	1.4	3.092

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	AB INITIO PHASING	THROUGHOUT	1.05	5.955	1.36	3943	394	83.45	0.2022	0.1976	0.2458	Random	10.1351

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	105
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SHELXDE	phasing

Sample
crystal of amyloid-beta residues 20-34 with L-isoaspartate at position 23

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)
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	29.2
Length b	4.87
Length c	4.87
Angle Alpha	90
Angle Beta	101.897
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	OTHER
Refinement Target	maximum liklihood
Overall B Value	10.135
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI CETA (4k x 4k)
Electron Dose (electrons/Å**2)	0.01

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Coot	0.8.9.1
MODEL REFINEMENT	PHENIX	1.14-3260

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.