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.
Cryo-EM structure of eGFP-tagged D13 assembled into scaffold-like particles from vaccinia virus
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.146
f_angle_d
0.581
f_chiral_restr
0.046
f_bond_d
0.005
f_plane_restr
0.004
Sample
Assembled scaffold-like particle of
Vaccinia virus D13
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Wait time: 10sec
Blot force: 0
Blot time: 5sec
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
285080
Reported Resolution (Å)
3.7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C3
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Map-to-model correlation
Overall B Value
167.04
Fitting Procedure
Details
Model building was proceeded by manually fitting the cryo-EM structure of D13 (PDB ID 7VFD) into our cryo-EM map using UCSF Chimera.
The model was su ...
Model building was proceeded by manually fitting the cryo-EM structure of D13 (PDB ID 7VFD) into our cryo-EM map using UCSF Chimera.
The model was subsequently inspected and adjusted in Coot.
Coordinate refinements were performed using the real-space refinement routine in the Phenix software suite.