5W52 | pdb_00005w52

MicroED structure of the segment, DLIIKGISVHI, from the RRM2 of TDP-43, residues 247-257

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		idealized 11-residue beta strand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH	8.5	310	50 mM CHES, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
1.51	18.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.81	α = 80.88
b = 4.73	β = 86.37
c = 15.83	γ = 89.78

Symmetry
Space Group	P 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		2017-01-19

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	1.4	15.6	73.4	0.203	0.213	0.992	3.34	9.019		1037		-3	21.481

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	1.48	62.1		1.451	1.562	0.333	0.92	6.712

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	idealized 11-residue beta strand	1.4	15.6	944	92	72.04	0.2655	0.2619	0.3065	RANDOM	33.756

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]
20.78	-1.04	-18.05	-25.77	-3.48	4.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.273
r_dihedral_angle_3_deg	7.47
r_dihedral_angle_1_deg	6.438
r_angle_refined_deg	1.211
r_angle_other_deg	0.776
r_chiral_restr	0.079
r_bond_other_d	0.017
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	84
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Sample
DLIIKGISVHI fibril

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument
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	24.81
Length b	4.73
Length c	4.73
Angle Alpha	89.78
Angle Beta	86.37
Angle Gamma	89.78

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	TVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å**2)	3.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI 20
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	TVIPS	F416
MODEL FITTING	Coot
MOLECULAR REPLACEMENT	Phaser
CRYSTALLOGRAPHY MERGING	XSCALE
MODEL REFINEMENT	REFMAC

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.