Table I.

X-Ray Crystal Structures Used for Validation and Overall Atomic Agreement

Codea	Resb (Å)	Lenc	pHd	Compound	Timee (s)	Atomsf	Agreeg (%)
1EJG26	0.54	46	7.0	Crambin	0.9	31	87
1GCI27	0.78	269	5.9	Subtilisin	11.3	185	99
1GDN28	0.81	242	6.0	Trypsin	19.0	167	85
1P9G29	0.84	41	5.5	Antifungal protein	0.9	20	90
1UCS30	0.62	64	7.5	Antifreeze protein RD1	1.3	76	91
1YK431	0.69	53	6.0	Rubredoxin	1.5	56	88
2B9732	0.75	140	7.4	Hydrophobin II	2.2	128	89
2H5C33	0.82	198	4.3	Alphalytic protease	9.0	163	85
3PYP34	0.85	125	4.8	Photoactive yellow protein	4.1	119	95

^aSuperscripts denote manuscript references.

^bResolution (Å) of the X-ray diffraction.

^cNumber of residues of the main macromolecular chain.

^dpH is taken from the PDB header (crystallization conditions).

^eRun time of Protonate3D in seconds on a 2 GHz Pentium IV.

^fNumber of –;OH, –SH, –NH_i, –CH₃, –CO₂, N(his) atoms with hydrogen occupancy ≥0.8.

^gThe percentage agreement of hydrogen placement to within 15° dihedral angle of experiment.