Table 3.

Selected parameters of the originally deposited (left column) and re-refined (right column) MBL structures described in the sections ‘Incorrect treatment of ligands’ and ‘Improvement of structural models after re-processing of the diffraction images’. Data prepared as for Table 1.

Protein	NDM-1		NDM-1		NDM-1		Bradyrhizobium diazoefficiens BJP-1
PDB accession code	4eyl	5n0h	4hky	6ex7	4rl0	5o2e	3m8t	5wcm
Resolution [Å]	74.95–1.90 (1.95–1.90)	74.95–1.90 (1.95–1.90)	74.23–2.00 (2.06–2.00)	74.20–1.951 (2.00–1.95)	67.86–1.30 (1.33–1.30)	67.86–1.30 (1.33–1.30)	22.21–1.33 (1.36–1.33)	50.00–1.20* (1.22 – 1.20)
No. of reflections refinement/Rfree	38308/2030	38308/2030	27161/1446	27008/1353	88894/4618	88894/4618	97262/5123	117432/6083
Completeness [%]	95.79(90.94)	95.79(90.94)	99.50(97.73)	91.72(66.00)	91.38(84.16)	91.38(84.16)	91.85 (89.24)	81.32 (26.78)
<Ι/σ> in the highest resolution shell	2.1	2.1	2.3	2.2	2.6	2.6	6.9	4.4
R / Rfree [%]	18.7/22.1	15.5/19.8	24.1/26.9	19.4/22.6	15.7/16.5	10.1/13.3	14.3/17.7	13.2/16.0
Protein molecules in the ASU	2	2	2	2	2	2	2	2
NCS restraints			Local	Local	-			-
ADP parametrization	Isotropic	Isotropic	Isotropic+TLS	Isotropic+TLS	Isotropic	Anisotropic	Anisotropic+TLS#	Anisotropic
No. atoms
Protein	3500	3520	3487	3498	3499	3705	4043	4031
Ligands	58	66	77	55	64	63	41	37
Water	161	398	136	178	645	676	690	829
Ramachandran statistics [%]
Favored/outliers	97.43/0.43	98.29/0.00	97.41/0.65	99.16/0.00	99.13/0.00	98.73/0.00	96.36/0.38	95.98/0.38
R.m.s. deviations from target values
Bond lengths [Å]	0.017	0.018	0.016	0.014	0.016	0.013	0.015	0.009
Bond angles [°]	1.35	1.80	1.80	1.58	2.58	1.62	1.61	1.40
Clashscore/percentile	7.42/90th	2.54/99th	9.15/86th	1.73/100th	7.15/70th	2.28/99th	3.08/97th	0.62/99th

^*The dataset was reprocessed with HKL-3000, and the resolution was extended. Auto-correction mode was used in data scaling which resulted in the elimination of non-informative reflections.

^#This was a redundant combination of ADP parameters.