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PDB Id
Uniprot Id
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Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
5YFP
pdb_00005yfp
10.2210/pdb5yfp/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
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MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Protein sample was applied onto a Quantifoil R1.2/1.3 golden grid and hold for 60 seconds, then blot for 2.5 seconds before plunging.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
343342
Reported Resolution (Å)
4.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
Exo70 (a.a.67-623) was first fit into the map with Situs as a rigid body. Then it was split as Exo70 (a.a.67-344) and Exo70 (a.a.345-623), and fit into the same position with Chimera.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å
2
)
50.0
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
2000
Maximum Defocus (nm)
3000
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
22500
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
RELION
1.4
IMAGE ACQUISITION
UCSFImage
4
CTF CORRECTION
RELION
1.4
MODEL FITTING
Situs
2.8
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Situs
2.8
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
Coot
0.8.2
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Chimera
1.10.1
MODEL REFINEMENT
Coot
0.8.2
MODEL REFINEMENT
PHENIX
1.11.1
MODEL FITTING
Coot
0.8.2
MODEL REFINEMENT
PHENIX
1.11.1
INITIAL EULER ASSIGNMENT
RELION
1.4
FINAL EULER ASSIGNMENT
RELION
1.4
CLASSIFICATION
RELION
1.4
RECONSTRUCTION
RELION
1.4
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
The defocus value of each image was determined by CTFFIND3.
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