ELECTRON MICROSCOPY

Sample

Ribonucleotide reductase from Synechoccus phage S-CBP4 bound with TTP

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details blot for 4 seconds before plunging
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 107885
Reported Resolution (Å) 3.46
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 FLEXIBLE FIT
Refinement Target ?
Overall B Value 74.37
Fitting Procedure ?
Details The sequence for the ribonucleotide reductase from Synechococcus phage S-CBP4 was retrieved from UniProt with accession number M1PRZ0. The sequence was used as input for AlphaFold2 prediction with the five default model parameters and a template date cutoff of 2020-05-14. As the five models were largely identical in the core region and differing only in the location of the C-terminal tail, the structure predicted with the first model parameter was used in the subsequent process. The predicted structure was first processed and docked into the unsharpened map in phenix. The 25 N-terminal residues and 45 C-terminal residues were then manually removed due to lack of cryo-EM density, and residues 26-426 were retained in the model. We observed unmodeled density at the specificity site, and based on solution composition, we modeled a TTP molecule. The TTP molecule with magnesium ion from the crystal structure of Bacillus subtilis RNR (pdb: 6mt9) was extracted and rigid body fit into the unmodeled density in Coot. The combined model was refined with the unsharpened and sharpened maps using phenix.real_space_refine, with a constraint applied on the magnesium ion coordinated by the triphosphate in TTP according to the original configuration. Residue and loop conformations in the resulting structure were manually adjusted in Coot to maximize fit to map and input for an additional round of real-space refinement in phenix with an additional restraint for the disulfide bond between C30 and C196. Due to poor density of the magnesium ion, it was removed when deposited into PDB.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 50
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS TALOS
Minimum Defocus (nm) 600
Maximum Defocus (nm) 2000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model OTHER
Nominal Magnification 79000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details Data was collected on a Thermo Fisher Talos Arcica Cryo-TEM with a Gatan K3 camera and BioQuantum energy filter.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 3.3.1
IMAGE ACQUISITION SerialEM 3.8
CTF CORRECTION cryoSPARC 3.3.1
MODEL FITTING PHENIX 1.20.1
INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1
FINAL EULER ASSIGNMENT cryoSPARC 3.3.1
RECONSTRUCTION cryoSPARC 3.3.1
MODEL REFINEMENT PHENIX 1.20.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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