Examples of the DPI using Rfree

Cruickshank, D. W. J.

doi:10.1107/97809553602060000697

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

pdf | chapter contents | chapter index | related articles

International Tables for Crystallography (2006). Vol. F. ch. 18.5, pp. 411-412 | 1 | 2 |

Section 18.5.7.3. Examples of the DPI using R_free

D. W. J. Cruickshank^a ^*^‡

^a Chemistry Department, UMIST, Manchester M60 1QD, England
Correspondence e-mail: dwj_cruickshank@email.msn.com

18.5.7.3. Examples of the DPI using R_free

| top | pdf |

As in the case of monoclinic thaumatin, for low-resolution structures the number of parameters may exceed the number of diffraction data. To circumvent this difficulty, it was proposed in Section 18.5.6.3 to replace $[p = n_{\rm obs} - n_{\rm params}]$ by $[n_{\rm obs}]$ and R by $[R_{\rm free}]$ in a revised formula (18.5.6.10) for the DPI. Table 18.5.7.3 shows examples for some structures for which both R and $[R_{\rm free}]$ were available. The second row for each protein shows the alternative values for $[(N_{i}/n_{\rm obs})^{1/2}]$ , $[R_{\rm free}]$ and the DPI $[\sigma (r, B_{\rm avg})]$ from (18.5.6.10).

Table 18.5.7.3| top | pdf |
Comparison of DPIs using R and R_free

The second row for each protein contains values appropriate to the DPI equation (18.5.6.10) using R_free.

Protein	$[N_{i}]$	$[n_{\rm obs}]$	$[(N_{i}/p)^{1/2}]$ , $[(N_{i}/n_{\rm obs})^{1/2}]$	$[C^{-1/3}]$	R, $[R_{\rm free}]$	$[d_{\min}]$ (Å)	DPI $[\sigma (r, B_{\rm avg})]$ (Å)	Luzzati $[\langle \Delta r\rangle]$ (Å)	Read $[\langle \Delta r\rangle]$ (Å)	Reference
Concanavalin A	2130	116712	0.148	1.099	0.128	0.94	0.034	0.06		(a)
Concanavalin A			0.135		0.148		0.036

γB-Crystallin	1708	26151	0.297	1.032	0.180	1.49	0.14	0.16	0.12	(b)
γB-Crystallin			0.256		0.204		0.14

βB2-Crystallin	1558	18583	0.356	∼1.032	0.184	2.10	0.25	0.21	0.17	(b)
βB2-Crystallin			0.290		0.200		0.22

Ribonuclease A with RI	4416	18859	1.922	1.145	0.194	2.50	1.85	0.32	0.57	(c)
Ribonuclease A with RI			0.484		0.286		0.69

Fab HyHEL-5 with HEWL	4333	11754	^†	1.111	0.196	2.65	—	0.30		(d)
Fab HyHEL-5 with HEWL			0.607		0.288		0.69

References: (a) Deacon et al. (1997)

; (b) Tickle et al. (1998a)

; (c) Kobe & Deisenhofer (1995)

; (d) Cohen et al. (1996)

^† $[(N_{i}/p)]$ negative.

For the structures with $[d_{\min} \leq 2.0\ \hbox{\AA}]$ , the DPI is much the same whether it is based on R or $[R_{\rm free}]$ .

Tickle et al. (1998a) have made full-matrix error estimates for isotropic restrained refinements of γB-crystallin with $[d_{\min} = 1.49\ \hbox{\AA}]$ and of βB2-crystallin with $[d_{\rm min} = 2.10\ \hbox{\AA}]$ . The DPI $[\sigma (r, B_{\rm avg})]$ calculated for the two structures is 0.14 and 0.25 Å with R in (18.5.6.9), and 0.14 and 0.22 Å with $[R_{\rm free}]$ in (18.5.6.10). The full-matrix weighted averages of $[\sigma_{\rm res}(r)]$ for all protein atoms were 0.10 and 0.15 Å, for only main-chain atoms 0.05 and 0.08 Å, for side-chain atoms 0.14 and 0.20 Å, and for water oxygens 0.27 and 0.35 Å. Again, the DPI gives reasonable overall indices for the quality of the structures.

For the complex of bovine ribonuclease A and porcine ribonuclease inhibitor (Kobe & Deisenhofer, 1995) with $[d_{\min} = 2.50\ \hbox{\AA}]$ , the number of reflections is only just larger than the number of parameters, so that $[(N_{i}/p)^{1/2} = 1.922]$ is very large, and the DPI with R gives an unrealistic 1.85 Å. With $[R_{\rm free}]$ , $[\sigma (r, B_{\rm avg}) =0.69\ \hbox{\AA}]$ .

The HyHEL-5–lysozyme complex (Cohen et al., 1996) had $[d_{\rm min} = 2.65\ \hbox{\AA}]$ . Here the number of reflections is less than the number of parameters, but the $[R_{\rm free}]$ formula gives $[\sigma (r, B_{\rm avg}) =0.69\ \hbox{\AA}]$ .

References

Cohen, G. H., Sheriff, S. & Davies, D. R. (1996). Refined structure of the monoclonal antibody HyHEL-5 with its antigen hen egg-white lysozyme. Acta Cryst. D52, 315–326.Google Scholar

Kobe, B. & Deisenhofer, J. (1995). A structural basis of the interactions between leucine-rich repeats and protein ligands. Nature (London), 374, 183–186.Google Scholar

Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998a). Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of γB- and βB2-crystallin. Acta Cryst. D54, 243–252.Google Scholar

International Tables for Crystallography (2006). Vol. F. ch. 18.5, pp. 411-412

Section 18.5.7.3. Examples of the DPI using Rfree

18.5.7.3. Examples of the DPI using Rfree

References

Section 18.5.7.3. Examples of the DPI using R_free

18.5.7.3. Examples of the DPI using R_free