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Fitting

If pre-existing atomic coordinates have been fitted into the map, please use this page to provide details about the STARTING models.

The resulting map-derived model consisting of transformed or 'de-novo' built atomic coordinates (that are in-frame with the map) can be submitted to the PDB after completion of the map deposition.

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Have you fitted a known PDB structure into the map?: Yes
No
   
PDB identifier:   e.g. 1ABC
PDB chain list: e.g. A, B
Fitting software list: e.g. Chimera, EMFit
Refinement protocol:    
Target criteria: e.g. R-factor
Overall B value (Å^2): e.g. 20 (in angstrom squared)
Refinement space:    
Details: e.g. The domains were separately fitted by manual docking using program O

Fitting of a known PDB structure

Indicate if a known PDB structure was fitted into the map.

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PDB identifier

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors, NMR experimental data and electron diffraction data and atomic models fitted into cryo-electron microscopical derived Coulomb density. Each entry has a unique PDB ID code.

Example: 1ABC
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PDB chain list

Each chain in a PDB entry represents a contiguous polypeptide (or polynucleotide), though there may be breaks that are not explicitly recorded (except in REMARK records) due to crystallographic ambiguity. If there is only one chain, it is usually denoted with a 'A' in the chain ID field; multichain entries are usually labelled 'A', 'B', etc. Proteases and their peptide-containing inhibitors are often labelled 'E' and 'I', respectively.

Example: A, B
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Fitting software

The software packages used in fitting and refinement. Various computer programs are available for refining biological macromolecules and fitting atomic models into observed densities derived by electron microscopy. Manual docking is widely used, where the fit of the model is judged by eye and corrected manually until the fit 'looks best'. Often this subjective fit is refined using various reciprocal-space or real-space targets. Direct alignment of observed projections to predefined models and a global fitting procedure operating in reciprocal space have also been used. A docking procedure that relies on a global analysis of real-space correlation between the calculated electron density from the atomic model and the observed density provided by electron microscopy works by identifying 'solution sets' rather than relying on a singular best fit.

Example: SITUS, EMFIT
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Refinement protocol

The method used to fit into the map or subsequent model refinement. If your model was a combination of rigid body and flexible fitting choose FLEXIBLE.

Example: RIGID BODY
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Target criteria

The target criteria used in the refinement. The goal of Various computer programs are available for positional refinement is to achieve a best fit between the atomic model and the Coulomb potential density. The quality of fit can be judged by using a cross-validated or free R value to optimise the model's phase accuracy. The target criteria for refinement can be that of trying to find the global minimum of the target. These can include efforts to incorporate thermal motion into refinement.

Example: R-factor
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Overall B value

The B or temperature factor is the parameter in an exponential expression by which the scattering of an atom is reduced as a consequence of vibration (or a simulated vibration resulting from atomic disorder). For isotropic motion the exponential factor is:

exp( -Biso sin**2 theta/lambda )
with Biso called the temperature factor, theta the angle of incidence, lambda is the wavelength.

Range: 0 to 500 (angstroms squared)
Example:20 (angstroms squared)
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Select refinement space

After the subjective 'fit' of the model into the electron microscope generated Coulomb potential density, as judged by eye,local refinement can be carried out using various RECIPROCAL space or REAL space targets.
These methods include:
Direct alignment of observed projections to predefined models and a global fitting procedure operating in RECIPROCAL space.
Global analysis of REAL-space correlation between the calculated electron density from atomic model and the observed density provided by electron microscopy. This procedure identifies solution sets rather than relying on a singular best fit.

Example: RECIPROCAL
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Fitting details

Additional details about the method used for fitting atomic models into density distributions.
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