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.
Vitification was performed on CFlat 1.2/1.3 300 mesh holey carbon grids with copper support.
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
95407
Reported Resolution (Å)
4.07
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Overall resolution 4.07 angstrom as estimated by the masked gold-standard FSC = 0.143 criterion in cryoSPARC. Unmasked FSC values are lower, consisten ...
Overall resolution 4.07 angstrom as estimated by the masked gold-standard FSC = 0.143 criterion in cryoSPARC. Unmasked FSC values are lower, consistent with expected effects of masking." in the details field.
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
60.06
Angular Rotation
-166.03
Map-Model Fitting and Refinement
Id
1 (8UHW)
Refinement Space
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
A existing structure's (PDB:8UHW) coordinates were relaxed using the Rosetta Fast Relax algorithm and refined against the EM density from cryoSPARC us ...
A existing structure's (PDB:8UHW) coordinates were relaxed using the Rosetta Fast Relax algorithm and refined against the EM density from cryoSPARC using Phenix and Coot.
Histidine residues coordinate the iron ion; short distances flagged as clashes correspond to metal coordination geometry.
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
48
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
130000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.7.0
CTF CORRECTION
cryoSPARC
4.7
MODEL FITTING
Coot
0.9.8.96
INITIAL EULER ASSIGNMENT
cryoSPARC
4.7.0
FINAL EULER ASSIGNMENT
cryoSPARC
4.7.0
CLASSIFICATION
cryoSPARC
4.7.0
RECONSTRUCTION
cryoSPARC
4.7.0
MODEL REFINEMENT
PHENIX
2.0_5936
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
Patch CTF was used on micrographs, final volume had global and local CTF estimation jobs performed on it.
94278
94,278 particles were used in final reconstruction. Particles were picked using cryoSPARC's automated filament tracer with particle diameter of 70Ang and spacing of 0.2