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.
De novo calcium channel hexamer, CalC6_3 with DHR extensions
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
Other
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
13.056
f_angle_d
1.795
f_chiral_restr
0.093
f_plane_restr
0.015
f_bond_d
0.012
Sample
CalC6_3 with DHR extension
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
67181
Reported Resolution (Å)
3.75
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Non Uniform Refinement
Refinement Type
Symmetry Type
POINT
Point Symmetry
C6
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
The design model was used as an initial reference for building the final cryo-EM structure. For the hexamer the design model of the CalC6_3 was used a ...
The design model was used as an initial reference for building the final cryo-EM structure. For the hexamer the design model of the CalC6_3 was used as an initial reference model fit with UCSF Chimera. Hexamer was refined using several rounds of relaxation and minimization, performed on the complete structures, which were manually inspected for errors each time using ISOLDE in UCSF ChimeraX, Coot, and PHENIX real-space refinement. The final model quality was analyzed using MolProbity.