3DDX | pdb_00003ddx

HK97 bacteriophage capsid Expansion Intermediate-II model

ELECTRON MICROSCOPY

Starting Model(s)

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

Sample
Bacteriophage HK97 Expansion Intermediate II

Specimen Preparation
Sample Aggregation State	PARTICLE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles
Reported Resolution (Å)	14
Resolution Method
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1OHG)
Refinement Space	RECIPROCAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Vector Reciprocal Space Target
Overall B Value
Fitting Procedure
Details	METHOD--manual and rigid body fitting. THE COORDINATES CONTAIN ONLY THE BACKBONE ATOMS. DURING RIGID BODY DOCKING OF THE PROTEIN MODEL INTO THE EM D ...	METHOD--manual and rigid body fitting. THE COORDINATES CONTAIN ONLY THE BACKBONE ATOMS. DURING RIGID BODY DOCKING OF THE PROTEIN MODEL INTO THE EM DENSITY, THE TWO SUBDOMAINS 104-125 AND 155-175 OF EACH SUBUNIT WERE ALLOWED TO MOVE INDEPENDENTLY FROM THE REMAINDER OF THE RESIDUES (THE CORE OF EACH SUBUNIT). THAT IS WHY THE CONNECTIVITY OF THOSE SEGMENTS WITH THE REST OF THE SUBUNIT IS NOT WELL-PRESERVED. REFINEMENT PROTOCOL--Rigid Body, Magnification Optimized using Van Der Waals Constraints and Real-space Correlation Coefficient

Data Acquisition

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI/PHILIPS CM200FEG
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	38000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	CNS
MODEL FITTING	O

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.