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.
Outer Membrane Cytochrome S Filament from Geobacter Sulfurreducens
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
24.324
r_long_range_B_refined
21.036
r_dihedral_angle_4_deg
16.913
r_dihedral_angle_3_deg
13.373
r_mcangle_it
12.846
r_mcbond_it
7.296
r_scbond_it
5.262
r_dihedral_angle_1_deg
2.884
r_angle_refined_deg
2.622
r_chiral_restr
0.196
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
24.324
r_long_range_B_refined
21.036
r_dihedral_angle_4_deg
16.913
r_dihedral_angle_3_deg
13.373
r_mcangle_it
12.846
r_mcbond_it
7.296
r_scbond_it
5.262
r_dihedral_angle_1_deg
2.884
r_angle_refined_deg
2.622
r_chiral_restr
0.196
r_bond_refined_d
0.012
r_gen_planes_refined
0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Outer Membrane Cytochrome S filament as a bacterial nanowire
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
462964
Reported Resolution (Å)
3.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
47.5
Angular Rotation
83.01
Map-Model Fitting and Refinement
Id
1
Refinement Space
RECIPROCAL
Refinement Protocol
OTHER
Refinement Target
maximum likelihood with phases
Overall B Value
Fitting Procedure
Details
Atomic model was built de novo visually and repeatedly rebuilt visually using Coot and SPDBV. After each round of manual rebuilding, the parameters o ...
Atomic model was built de novo visually and repeatedly rebuilt visually using Coot and SPDBV. After each round of manual rebuilding, the parameters of the atomic model underwent stereochemically restrained reciprocal space refinement, using either Refmac5 or Phenix.autobuild or both, using as a reference the amplitudes and phases of the Fourier transform of a portion of the cryoEM reconstruction. For convenience, a single-subunit model was initially built to fit an approximation of the reference map in space group P4(3), which was subsequently replaced by a three-subunit model, using the authentic helical parameters of the map. one of the two axial ligands for HEM 505 is ne2 of his 41 from a neighboring helical-symmetry-related protein chain.