Improved estimates of coordinate error for molecular replacement.
Acta Crystallogr D Biol Crystallogr
; 69(Pt 11): 2209-15, 2013 Nov.
Article
en En
| MEDLINE
| ID: mdl-24189232
ABSTRACT
The estimate of the root-mean-square deviation (r.m.s.d.) in coordinates between the model and the target is an essential parameter for calibrating likelihood functions for molecular replacement (MR). Good estimates of the r.m.s.d. lead to good estimates of the variance term in the likelihood functions, which increases signal to noise and hence success rates in the MR search. Phaser has hitherto used an estimate of the r.m.s.d. that only depends on the sequence identity between the model and target and which was not optimized for the MR likelihood functions. Variance-refinement functionality was added to Phaser to enable determination of the effective r.m.s.d. that optimized the log-likelihood gain (LLG) for a correct MR solution. Variance refinement was subsequently performed on a database of over 21,000 MR problems that sampled a range of sequence identities, protein sizes and protein fold classes. Success was monitored using the translation-function Z-score (TFZ), where a TFZ of 8 or over for the top peak was found to be a reliable indicator that MR had succeeded for these cases with one molecule in the asymmetric unit. Good estimates of the r.m.s.d. are correlated with the sequence identity and the protein size. A new estimate of the r.m.s.d. that uses these two parameters in a function optimized to fit the mean of the refined variance is implemented in Phaser and improves MR outcomes. Perturbing the initial estimate of the r.m.s.d. from the mean of the distribution in steps of standard deviations of the distribution further increases MR success rates.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Secuencia de Aminoácidos
/
Sustitución de Aminoácidos
/
Bases de Datos de Proteínas
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Relación Señal-Ruido
Tipo de estudio:
Clinical_trials
/
Prognostic_studies
Idioma:
En
Revista:
Acta Crystallogr D Biol Crystallogr
Año:
2013
Tipo del documento:
Article
País de afiliación:
Reino Unido