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Fitting of L11 protein in the low resolution cryo-EM map of E.coli 70S ribosome
ELECTRON MICROSCOPY
NMR Refinement
Method
Details
Software
Molecular Modeling based on crystal structures
Conformational changes occur in protein L11 when it is bound to 70S
ribosome. This changed conformation was modeled based on the fitting
of the crystal coordinates to the low resolution ribosome map and
energy minimizing the fitted structures.
IRIS Explorer
Additional NMR Experimental Information
Details
This structure was generated by fitting the X-ray crystal structure of
L11 into the 70S E. coli ribosome map. L11 (linker region between N and
C terminal) was modeled to accommodate the observed densities.
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
data analysis
IRIS Explorer
3.5
Numerical Algorithms Group, Inc
2
data analysis
O
5.10
Jones, Zou, Cowan, Kjeldgaard
3
processing
SPIDER
4.48
Frank
4
data analysis
Insight II
1998
Biosym/MSI Inc.
Sample
70S ribosome
Specimen Preparation
Sample Aggregation State
PARTICLE
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
36113
Reported Resolution (Å)
18
Resolution Method
FSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
VISUAL AGREEMENT
Overall B Value
Fitting Procedure
Details
REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting
the X-ray crystal structure of L11 into the 70S E. coli ribosome map. L1 ...
REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting
the X-ray crystal structure of L11 into the 70S E. coli ribosome map. L11
(linker region between N and C terminal) was modeled to accommodate the
observed densities. Conformational changes occur in protein L11 and EF-G due to
the binding of EF-G to the 70S ribosome. These changed conformations were
modeled based on the fitting of the crystal coordinates to the low resolution
ribosome map (factor-bound) and energy minimizing the fitted structures.