Home
About
Browse
Covid-19
Organism Classification
Alphafold Collection
Virus Classification
Indian Data
Contact
Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
7U65
pdb_00007u65
10.2210/pdb7u65/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
dGTPase hexamer bound to six copies of Gp1.2
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
?
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
114127
Reported Resolution (Å)
2.8
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
E. coli dGTPase crystal structure (PDB ID: 4XDS) and T7 bacteriophage NMR structure (PDB ID: 2MDP) models were fit into the EM map using Chimera for subsequent building. After an initial round of real-space refinement, the Gp1.2 N-terminus was re-built into the density using Coot.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å
2
)
54
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TALOS ARCTICA
Minimum Defocus (nm)
750
Maximum Defocus (nm)
1750
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
45000
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
RELION
?
CTF CORRECTION
CTFFIND
4.1
MODEL FITTING
PHENIX
?
MODEL REFINEMENT
PHENIX
?
INITIAL EULER ASSIGNMENT
RELION
?
FINAL EULER ASSIGNMENT
RELION
?
CLASSIFICATION
RELION
?
RECONSTRUCTION
RELION
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?