Data Item _refine.overall_SU_ML

General

Item name
_refine.overall_SU_ML
Category name
refine
Attribute name
overall_SU_ML
Required in PDB entries
no
Used in current PDB entries
Yes, in about 55.7 % of entries

Item Description

The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigmaX)2 gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 Na (sigmaX)2 = --------------------------------------------------------- 8 pi2 sumi {[1/Sigma - (Eo)2 (1-m2)](SUM_AS)s2} Na = number of atoms Eo = normalized structure factors m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector SUM_AS = (sigmaA)2/Sigma2 Sigma = (sigma{E;exp})2 + epsilon [1-(sigmaA)2] sigma{E;exp} = experimental uncertainties of normalized structure factors sigmaA = <cos 2 pi s deltax> SQRT(SigmaP/SigmaN) estimated using maximum likelihood SigmaP = sum{atoms in model} f2 SigmaN = sum{atoms in crystal} f2 f = atom form factor deltax = expected error epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html

Additional Descriptive Information for Depositors

               The overall standard uncertainty (estimated standard deviation)
               of the positional parameters based on a maximum likelihood
               residual.

               The overall standard uncertainty (sigma~X~)^2^ gives an
               idea of the uncertainty in the position of averagely
               defined atoms (atoms with B values equal to average B value)

                     3                         N~a~
    (sigma~X~)^2^  = ---------------------------------------------------------
                     8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^}

               N~a~           = number of atoms
               E~o~           = normalized structure factors
               m              = figure of merit of phases of reflections
                                included in the summation
               s              = reciprocal-space vector

               SUM_AS         = (sigma~A~)^2^/Sigma^2^
               Sigma          = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
               sigma~{E;exp}~  = experimental uncertainties of normalized
                                structure factors
               sigma~A~        =  SQRT(Sigma~P~/Sigma~N~)
                                estimated using maximum likelihood
               Sigma~P~        = sum~{atoms in model}~ f^2^
               Sigma~N~        = sum~{atoms in crystal}~ f^2^
               f               = atom form factor
               delta~x~        = expected error
               epsilon         = multiplicity of diffracting plane

               summation is over all reflections included in refinement

               Ref: (sigma_A estimation) "Refinement of macromolecular
                    structures by the maximum-likelihood method",
                    Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
                    Acta Cryst. D53, 240-255.

                    (SU ML estimation) Murshudov, G. N. & Dodson,
                    E. J. (1997). Simplified error estimation a la
                    Cruickshank in macromolecular crystallography.
                    CCP4 Newsletter on Protein Crystallography, No. 33,
                    January 1997, pp. 31-39.

                   http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html

Data Type

Data type code
float
Data type detail
float item types are the subset of numbers that are the floating numbers.
Primitive data type code
numb
Regular expression
-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?

Advisory Boundary Conditions

Minimum Value Maximum Value
0 0.6