SPACI score report for 2ydn in ASTRAL 2.06:

PDB Entry: 2ydn
SPACI score: 0.52
AEROSPACI score: 0.52

Experiment type: XRAY
Resolution: 1.88
R-factor: 0.165
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: 1.309
WCK2 WHAT_CHECK Ramachandran: -0.797
WCK3 WHAT_CHECK Chi angles: 0.113
WCK4 WHAT_CHECK Backbone: 3.438

Note: Here are links to pages about PROCHECK and WHAT_CHECK.

Here is the full WHAT_CHECK report on this protein (linked from the WHAT_CHECK site).