7VI5 | pdb_00007vi5

Electron crystallographic structure of TIA-1 prion-like domain, wild type sequence

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VI4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.57	α = 90
b = 43.57	β = 90
c = 9.63	γ = 120

Symmetry
Space Group	P 65

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	7VI4	1.761	18.866	1.42	1149	114	99.91	0.2839	0.2772	0.2842	0.3473	0.3584	12.1368

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	9.935
f_angle_d	1.072
f_chiral_restr	0.08
f_bond_d	0.009
f_plane_restr	0.005

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

Sample
Region 2 peptides (G377-Q386) of TIA-1 prion-like domain, wild-type

Specimen Preparation
Sample Aggregation State	FILAMENT

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	43.57
Length b	43.57
Length c	43.57
Angle Alpha	120
Angle Beta	90
Angle Gamma	120

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

Data Acquisition
Detector Type	DIRECT ELECTRON DE-64 (8k x 8k)
Electron Dose (electrons/Å**2)	0.02

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL CRYO ARM 300
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

EM Software
Task	Software Package	Version
MODEL REFINEMENT	PHENIX

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.