Table 2.

Structure quality indicators for β-galactosidase structures. β-galactosidase structures investigated in the present study were uploaded to the MolProbity server (http://molprobity.biochem.duke.edu) to extract the quantities presented below. The results show that the cMDFF- and ReMDFF-refined structures not only exhibit good measures of fit, but also improve the clash score and rotamer geometries, relative to the de novo and initial structures, while incurring only a small expense in Ramachandran statistics, bad angles, and Cβ deviations.

DOI: http://dx.doi.org/10.7554/eLife.16105.015

	de novo (Bartesaghi et al., 2014)	Refined de novo	Initial	Direct MDFF	cMDFF	ReMDFF
Clashscore	53.7	0.0	0.0	0.0	0.0	0.0
Poor rotamers (%)	11.6	3.8	4.2	3.0	4.4	1.37
Favored rotamers (%)	67.4	90.8	87.8	92.1	89.8	95.3
Ramachandran outliers (%)	0.2	0.7	2.7	3.0	1.6	2.7
Ramachandran favored (%)	97.4	95.8	91.1	91.1	94.4	90.9
MolProbity	3.14	1.23	1.49	1.38	1.37	1.13
C$\beta$ deviations (%)	0.0	0.05	4.92	0.18	0.29	0.39
Bad bonds (%)	0.09	0.04	3.61	0.02	0.01	0.03
Bad angles (%)	0.03	0.60	3.98	0.63	0.49	0.37
RMS distance (Å)	0.007 (0.025%)	0.019 (0%)	0.035 (0.237%)	0.022 (0%)	0.019 (0%)	0.021 (0%)
RMS angle (degrees)	1.1 (0.009%)	2.2 (0.009%)	3.6 (1.177%)	2.4 (0.103%)	2.1 (0.018%)	2.3 (0.085%)
Cis prolines (%)	8.06	8.06	6.45	6.45	6.45	8.06
Cis non-prolines (%)	1.15	1.15	0.0	0.0	1.15	0.0