Experiment: 7RVD

ELECTRON CRYSTALLOGRAPHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.5 M zinc acetate, 15% ethanol, 0.2 M MES, pH 6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 4.87	α = 94.65
b = 10.17	β = 90.73
c = 31.29	γ = 101.15

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	electron	100	CMOS	TVIPS TEMCAM-F416		2016-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	OTHER	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	10.391	93.9	0.167	0.197	0.988	3.99	2.996		2977			4.54

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	1.03	94.7		0.514	0.65	0.742	1.33	2.433

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	AB INITIO PHASING	THROUGHOUT	1.003	10.391	2.05	2935	265	93.74	0.2056	0.2011	0.2177	0.2499	0.2557	8.4907

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.249
f_angle_d	0.92
f_chiral_restr	0.096
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	79
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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

Sample
Major prion protein

Specimen Preparation
Sample Aggregation State	3D ARRAY

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	1.003
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	4.87
Length b	10.17
Length c	10.17
Angle Alpha	101.15
Angle Beta	90.73
Angle Gamma	101.15

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

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI F30
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)	300
Imaging Details

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.