3DIK | pdb_00003dik

Pseudo-atomic model of the HIV-1 CA hexameric lattice

ELECTRON CRYSTALLOGRAPHY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GWP
experimental model	PDB	1A43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.7	α = 90
b = 92.7	β = 90
c = 110	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron						M	SINGLE WAVELENGTH

Refinement

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	219
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Sample
HIV-1 CA PROTEIN R18L MUTANT
Sample Components
HIV-1 CA HEXAMER
HIV-1 CA DIMER

Specimen Preparation
Sample Aggregation State	2D ARRAY
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details	Washed with 0.1M KCl, blotted briefly, and plunged into liquid ethane

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	9
Resolution Method
Other Details	THIS MODDEL CONTAINS CA ATOMS ONLY. THE TWO DOMAINS UNP RESIDUES 133-280 AND UNP RESIDUES 281-351 WERE ALLOWED TO MOVE INDEPENDENTLY. THAT IS WHY THE CONNECTIVITY BETWEEN THEM IS NOT WELL-PRESERVED. MRC AND CCP4 PROGRAMS WERE USED.
Refinement Type
Symmetry Type	2D CRYSTAL

Map-Model Fitting and Refinement
Id	1 (1GWP, 1A43)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--RIGID BODY

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	10

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	90
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)	40.3
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	52000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	SITUS COLACOR
MODEL FITTING	SITUS COLORES
RECONSTRUCTION	MRC