5WKB | pdb_00005wkb

MicroED structure of the segment, NFGEFS, from the A315E familial variant of the low complexity domain of TDP-43, residues 312-317

ELECTRON CRYSTALLOGRAPHY

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Batch	7.5	298	1x PBS, pH 7.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.77	α = 90
b = 17.42	β = 90
c = 4.9	γ = 90

Symmetry
Space Group	P 21 21 2

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		2016-08-26

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	21.39	88.7	0.283	0.299	0.992	4.64	9.452		2004		-3	7.454

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.03	78		0.993	1.085	1.07	4.809

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	AB INITIO PHASING	THROUGHOUT	1	21.39	1801	203	88.71	0.2251	0.2201	0.2697	RANDOM	5.061

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]
0.18			0.16		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.684
r_sphericity_free	25.539
r_dihedral_angle_3_deg	7.324
r_dihedral_angle_1_deg	7.068
r_sphericity_bonded	3.846
r_rigid_bond_restr	1.516
r_angle_refined_deg	1.085
r_angle_other_deg	0.911
r_chiral_restr	0.135
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	50
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms

Software

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

Sample
Segment from TDP-43

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)	1
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	42.77
Length b	17.42
Length c	17.42
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

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 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	TVIPS F416 CMOS CAMERA
MODEL FITTING	Coot
MODEL REFINEMENT	REFMAC
MOLECULAR REPLACEMENT	SHELXD
CRYSTALLOGRAPHY MERGING	XSCALE

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