5K2G | pdb_00005k2g

Structure of GNNQQNY from yeast prion Sup35 in space group P21 determined by MicroED

ELECTRON CRYSTALLOGRAPHY

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH	7	273	water

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 22.87	α = 90
b = 4.93	β = 107.77
c = 24.18	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	CCD	TVIPS F416 CMOS CAMERA		2016-02-03

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	TECNAI F20 TEM	0.0251

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		THROUGHOUT	1.1	23.03	1997	222	92.54	0.1902	0.1866	0.2242	RANDOM	5.098

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]
0.23		0.08	-0.56		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	60.232
r_sphericity_free	13.935
r_dihedral_angle_3_deg	9.053
r_dihedral_angle_1_deg	6.832
r_sphericity_bonded	3.759
r_angle_refined_deg	1.337
r_angle_other_deg	0.979
r_mcangle_it	0.629
r_rigid_bond_restr	0.467
r_mcbond_it	0.466
r_mcbond_other	0.435
r_chiral_restr	0.075
r_bond_refined_d	0.019
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	59
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Sample
Prion fibril composed of a 7-residue segment of Sup35

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Plunged into liquid ethane (FEI VITROBOT MARK IV)

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details	The density map was obtained using measured diffraction intensities and phases acquired from crystallographic direct methods program SHELXD.
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	22.87
Length b	4.93
Length c	4.93
Angle Alpha	90
Angle Beta	107.77
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	OTHER
Refinement Target	maximum likelihood
Overall B Value	5.1
Fitting Procedure
Details

Data Acquisition
Detector Type	TVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å**2)	0.01

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	EM-Menu	1
DIFFRACTION INDEXING	XDS	Oct 15, 2015
MODEL FITTING	Coot	0.8.2
OTHER	SHELXD	2013/2
MODEL REFINEMENT	refmac5	5.8.0135
CRYSTALLOGRAPHY MERGING	SCALEPACK	1.98.7
RECONSTRUCTION	SHELXD	2013/2

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