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.
Grids were frozen on a manual plunger at the Scripps Research Institute Core Microscopy Facility in a 4 degrees C cold room humidified to >95%.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
236339
Reported Resolution (Å)
3
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (5VY5, 5MA6, 5MA6)
Refinement Space
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
PDB models 5vy5 and 5ma6 were used as starting points. These models were mutated to match the sequence of the DARPin-aldolase platform in complex wit ...
PDB models 5vy5 and 5ma6 were used as starting points. These models were mutated to match the sequence of the DARPin-aldolase platform in complex with GFP that were used. The PDB models were docked into the cryoEM density using Chimera fit into map function. No model refinement was used.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
GATAN K2 SUMMIT (4k x 4k)
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
2.3
2.3
1.1
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
10000
Maximum Defocus (nm)
30000
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
165000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
IMAGE ACQUISITION
SerialEM
IMAGE ACQUISITION
EPU
CTF CORRECTION
CTFFIND
4.1.10
CTF CORRECTION
RELION
3.0 beta 2
MODEL FITTING
UCSF Chimera
1.12
INITIAL EULER ASSIGNMENT
RELION
3.0 beta 2
FINAL EULER ASSIGNMENT
RELION
3.0 beta 2
RECONSTRUCTION
RELION
3.0 beta 2
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
First whole micrograph correction with CtfFind4. Then per particle CTF Refinement in Relion.
851776
Manually picked particles were used to generate references for autopicking. Particles from all three microscopy sessions were processed together.
Microscope session 1 - 358,381 particles
Microscope session 2 - 64,368 particles
Microscope session 3 - 402,427 particles