9T03 | pdb_00009t03

Human PCNA in complex with a anti-PCNA DNA aptamer

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AXC

Sample
Human PCNA in the complex with anti-PCNA aptamer
Sample Components
proliferating cell nuclear antigen (PCNA)
anti-PCNA ptamer

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	blot force -1, blot time 3.0 s, drain time 0.0 s

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	929750
Reported Resolution (Å)	2.79
Resolution Method	FSC 0.143 CUT-OFF
Other Details	particles were reference-based motion-corrected before the final refinement
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1AXC, 1AXC, 1AXC)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial rigid-body fitting for PCNA was performed using ChimeraX. Fitting for the anti-PCNA aptamer was done using Coot. The overall geometry was guessed based on the double-stranded aptamer portion and protruding densities for T28 and G38.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2400
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.1.2
IMAGE ACQUISITION	EPU	2.10.0.1941REL
CTF CORRECTION	cryoSPARC	4.1.2
MODEL FITTING	UCSF ChimeraX
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	cryoSPARC	4.1.2
FINAL EULER ASSIGNMENT	cryoSPARC	4.1.2
CLASSIFICATION	cryoSPARC	4.1.2
RECONSTRUCTION	cryoSPARC	4.4.0
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF, global and local CTF refinement	637535	Initial set of particles was picked from a set of 500 micrographs by the Blob Tuner. These particles were 2D-classified and then used as an input for the TOPAZ model and Topaz extract picker.