5K2F | pdb_00005k2f

Structure of NNQQNY from yeast prion Sup35 with cadmium acetate determined by MicroED

ELECTRON CRYSTALLOGRAPHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	273	1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M cadmium sulfate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 22.074	α = 90
b = 4.932	β = 104.29
c = 23.51	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	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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	90	84.5	0.18	5.1	4.6		2564

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.08	66		0.282		3.3	365

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	22.79	2308	253	80.97	0.2223	0.2203	0.2415	RANDOM	6.444

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		0.36	-0.29		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	60.278
r_dihedral_angle_3_deg	8.34
r_sphericity_free	6.512
r_dihedral_angle_1_deg	5.527
r_sphericity_bonded	4.945
r_angle_refined_deg	1.688
r_angle_other_deg	0.957
r_rigid_bond_restr	0.84
r_mcbond_it	0.502
r_mcangle_it	0.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	60.278
r_dihedral_angle_3_deg	8.34
r_sphericity_free	6.512
r_dihedral_angle_1_deg	5.527
r_sphericity_bonded	4.945
r_angle_refined_deg	1.688
r_angle_other_deg	0.957
r_rigid_bond_restr	0.84
r_mcbond_it	0.502
r_mcangle_it	0.233
r_mcbond_other	0.189
r_chiral_restr	0.124
r_bond_refined_d	0.021
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	55
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	8

Software

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

Sample
Prion fibril composed of a 6-residue segment of Sup35 and cadmium

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	22.074
Length b	4.932
Length c	4.932
Angle Alpha	90
Angle Beta	104.29
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	OTHER
Refinement Target	maximum likelihood
Overall B Value	6.44
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	Denzo	1.98.7
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

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.