Table 5.

Effect of EM, MD, and CONCOORD analyses

Method	Average RMSD	Correct	Wrong	Avg. pKa Glu 35 (std. dev.)	Avg. pKa Asp 52 (std. dev.)	Avg. titr. Glu 35	Avg. titr. Asp 52
X-ray struct. ɛ = 8	1.10	30	2	5.61 (0.40)	3.70 (0.91)	5.70	3.80
X-ray struct. ɛ = 4	1.49	28	5	6.32 (0.79)	4.47 (1.34)	6.40	4.40
X-ray struct. ɛ = 16	0.66	1	0	4.78 (0.25)	3.66 (0.59)	4.90	3.70
EM	1.01	19	0	5.42 (0.30)	4.13 (1.03)	5.50	4.20
Avg. MD	1.09	0	0	2.86 (0.78)	3.21 (0.49)	2.90	3.30
Avg. MD + EM	1.13	0	0	2.69 (0.74)	3.20 (0.49)	2.70	3.30
Avg. CC	0.94	13	0	5.28 (0.31)	4.02 (0.72)	5.40	4.20
Avg. CC + EM	0.97	12	1	5.24 (0.36)	4.04 (0.82)	5.30	4.20
89 snapshots (2LZT)	0.96	0	0	3.60 (0.64)	2.88 (0.68)	3.70	2.90
89 snapshots (5LYZ)	1.18	2	1	2.82 (0.89)	2.27 (1.01)	2.90	2.30

Average RMSD, average between calculated and experimentally measured pKa values for all groups; Correct, number of the original 41 X-ray structures where Glu 35 was identified as the proton donor after EM, MD, or CC analysis, using the local ID criteria; Wrong, number of the original 41 X-ray structures where Asp 52 was identified as the proton donor after EM, MD, or CC analysis, using the local ID criteria; EM, final structure of a steepest descent energy minimization; MD, average structure of the last 100ps of a 200ps molecular dynamics simulation; MD + EM, energy minimized (steepest descent) structure of the MD structures; CC, Average structure of 2000 CONCOORD structures; CC + EM, Energy minimized (steepest descends) of the CC structures.