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Organism Classification
Alphafold Collection
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Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
8RUP
pdb_00008rup
10.2210/pdb8rup/pdb
Download file
FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Human CPC localisation module in complex with Xenopus H3.T3p-nucleosome
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3 s blotting time, -10 force, no wait time.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
119063
Reported Resolution (Å)
2.42
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Final reconstruction performed following particle polishing in Relion and subsequent re-import in CryoSPARC. The CPC distal region was then further locally refined and sharpened using DeepEMhancer. The resolution value given for the raw final reconstruction before local refinement.
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation coefficient
Overall B Value
59.74
Fitting Procedure
?
Details
?
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å
2
)
43.86
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
2300
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
58009
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.4.0
CTF CORRECTION
cryoSPARC
4.4.0
MODEL FITTING
UCSF Chimera
1.14
MODEL FITTING
Coot
0.9.8.1
MODEL REFINEMENT
PHENIX
1.20.1
CLASSIFICATION
cryoSPARC
4.4.0
RECONSTRUCTION
cryoSPARC
4.4.0
RECONSTRUCTION
RELION
4.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF amplitude correction first performed following movie motion correction, and CTF parameters were later refined during the refinement of the final reconstruction
