Table 2. Model-refinement statistics R factor, R _free, ΔR = R _free − R and −LL_free, and ‘clashscore’ and ‘MolProbity score’ from model validation using MolProbity .

Percentages in parentheses indicate how the score compares amongst structures of comparable resolution (larger is better). Refinement statistics were calculated using REFMAC5 (original R/R _free values in the PDB files were 0.127/0.307 for 1ydz and 0.129/0.153 for 2w72). Note that (unnormalized) values of −LL_free are not comparable for different structures and are quoted for the model achieved by optimizing R _free (when using external restraints).

Model	R	Rfree	ΔR	−LLfree	Clashscore	MolProbity score
Original (1ydz)	0.1388	0.2630	0.1242	5389	39.02 (67%)	3.20 (77%)
Reference (2w72)	0.2395	0.2465	0.0070	53516	11.54 (19%)	1.80 (35%)
Refined without external restraints	0.1391	0.2594	0.1203	5367	28.41 (86%)	3.08 (82%)
Refined with local NCSR without external restraints	0.1517	0.2422	0.0905	5287	21.22 (91%)	2.74 (94%)
Local NCSR and α-helix restraints	0.1576	0.2381	0.0805	5300	21.00 (91%)	2.68 (96%)
Local NCSR and external main-chain restraints	0.1722	0.2342	0.0620	5271	15.81 (97%)	2.44 (98%)
Local NCSR and external main/side-chain restraints	0.1574	0.2304	0.0730	5245	16.69 (97%)	2.45 (98%)