7U65 | pdb_00007u65

Structure of E. coli dGTPase bound to T7 bacteriophage protein Gp1.2

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XDS
experimental model	PDB	2MDP

Sample
dGTPase hexamer bound to six copies of Gp1.2
Sample Components
dGTP triphosphohydrolase
Gene 1.2 protein

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	114127
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	D3

Map-Model Fitting and Refinement
Id	1 (4XDS, 2MDP)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	E. coli dGTPase crystal structure (PDB ID: 4XDS) and T7 bacteriophage NMR structure (PDB ID: 2MDP) models were fit into the EM map using Chimera for subsequent building. After an initial round of real-space refinement, the Gp1.2 N-terminus was re-built into the density using Coot.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	54

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	750
Maximum Defocus (nm)	1750
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	45000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	PHENIX
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	RELION
FINAL EULER ASSIGNMENT	RELION
CLASSIFICATION	RELION
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		732832	Laplacian-of-Gaussian auto-picking