Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Two 3uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
48209
Reported Resolution (Å)
1.56
Resolution Method
FSC 0.143 CUT-OFF
Other Details
These 48209 particles refined to approx. 2.2 A with I1 symmetry, and subsequent refinements of beam tilt and per-particle CTF brought the resolution t ...
These 48209 particles refined to approx. 2.2 A with I1 symmetry, and subsequent refinements of beam tilt and per-particle CTF brought the resolution to 1.8 A. Further particle-polishing and subsequent re-refinement of CTF brought the resolution to 1.70 A and a final reconstruction using Ewald sphere correction ended at 1.56 A. The map used for modeling was sharpened using the volume whitening routine in cisTEM.
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1 (5UF6)
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Least-squares residual
Overall B Value
Fitting Procedure
Details
Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embed ...
Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embedded CNS was used for molecular dynamics optimization (1st round) and stereochemically-restrained all-atom least-squares optimization.
Data Acquisition
Detector Type
FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)
30
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
-800
Maximum Defocus (nm)
-2600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
155000
Calibrated Magnification
154400
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Coma-free alignment and objective astigmatism where corrected using Sherpa (Thermo Fisher, Inc.).
EM Software
Task
Software Package
Version
PARTICLE SELECTION
DoG Picker
IMAGE ACQUISITION
EPU
CTF CORRECTION
Gctf
MODEL FITTING
Coot
0.8.9.2
INITIAL EULER ASSIGNMENT
RELION
3.0
FINAL EULER ASSIGNMENT
RELION
3.0
CLASSIFICATION
RELION
3.0
RECONSTRUCTION
RELION
3.0
MODEL REFINEMENT
RSRef
0.5.8
MODEL REFINEMENT
CNS
1.3
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING ONLY
75316
DoG (Difference of Gaussian) Picker was used for initial automated particle selection. Templates were then generated by 2D classification, followed by particle template selection in Relion 3.0.