Data Item _refine.overall_SU_ML


Item name
Category name
Attribute name
Required in PDB entries
Used in current PDB entries
Yes, in about 60.4 % 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 N_a (sigmaX)2 = ----------------------------------------------------- 8 pi2 sumi {[1/Sigma - (E_o)2 (1-m2)](SUM_AS)s2} SUM_AS = (sigma_A)2/Sigma2) N_a = number of atoms Sigma = (sigma_{E;exp})2 + epsilon [1-{sigma_A)2] E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f2 Sigma_N = sum_{atoms in crystal} f2 f = form factor of atoms delta_x = expected error m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector epsilon = multiplicity of the 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.

Data Type

Data type code
Data type detail
float item types are the subset of numbers that are the floating numbers.
Primitive data type code
Regular expression


Alias Item Name Dictionary Name Dictionary Version
_refine.ebi_Overall_ESU_ML ebi_extensions 1.0