Experiment: 5UPW

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XFX

Sample
HIV-1 Capsid Protein Assembly

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	The assembled sample (1.5 microliter) was applied to the carbon side of a glow discharged perforated Quantifoil grid, followed by application of 3 mic ...	The assembled sample (1.5 microliter) was applied to the carbon side of a glow discharged perforated Quantifoil grid, followed by application of 3 microliter of low salt buffer (100 milimolar NaCl, 50 milimolar Tris pH 8.0) on the back side of the grid, and blotting, from the back side, with a filter paper, before plunge-freezing in liquid ethane

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	38452
Reported Resolution (Å)	5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	6.94
Angular Rotation	-31.13

Map-Model Fitting and Refinement
Id	1 (4XFX)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	41

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	SIDE ENTRY, EUCENTRIC
Nominal Magnification	31000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN	2
CTF CORRECTION	CTFFIND	3
MODEL FITTING	MDFF	2.10
MODEL REFINEMENT	Rosetta	3.0
INITIAL EULER ASSIGNMENT	IHRSR
FINAL EULER ASSIGNMENT	RELION	1.4
RECONSTRUCTION	RELION	1.4

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		39712