wwPDB validation report of PDB entry 6Z9G

Periplasmic [NiFeSe] hydrogenase, small subunit

Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing

Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|-|Fc| maps and occupancy factors were refined for disordered residues; TLS rigid body refinement of atomic displacement parameters were refined; Non-crystallographic symmetry restraints were used and weight optimization was applied to lower the gap between the R-factor and the R-free.
Periplasmic [NiFeSe] hydrogenase, small subunit (E.C.1.12.7.2), Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing (E.C.1.12.7.2)
Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2
(chain "A" and (resid 7 through 20 or resid 22 through 57 or resid 59 through 76 or resid 78 through 241 or resid 243 through 285))
(chain "C" and (resid 7 through 20 or resid 22 through 57 or resid 59 through 76 or resid 78 through 241 or resid 243 through 285))
(chain "E" and (resid 7 through 20 or resid 22 through 57 or resid 59 through 76 or resid 78 through 241 or resid 243 through 285))
(chain "G" and (resid 7 through 20 or resid 22 through 57 or resid 59 through 76 or resid 78 through 241 or resid 243 through 285))
(chain "B" and (resid 15 through 74 or resid 76 through 162 or resid 164 through 204 or resid 206 through 272 or resid 274 through 384 or resid 386 through 488 or resid 490 through 500 or resid 502 or resid 504))
(chain "D" and (resid 15 through 74 or resid 76 through 162 or resid 164 through 204 or resid 206 through 272 or resid 274 through 384 or resid 386 through 488 or resid 490 through 500 or resid 502 or resid 504))
(chain "F" and (resid 15 through 74 or resid 76 through 162 or resid 164 through 204 or resid 206 through 272 or resid 274 through 384 or resid 386 through 488 or resid 490 through 500 or resid 502 or resid 504))
(chain "H" and (resid 15 through 74 or resid 76 through 162 or resid 164 through 204 or resid 206 through 272 or resid 274 through 384 or resid 386 through 488 or resid 490 through 500 or resid 502 or resid 504))
binding site for residues H2S B 503 and SEC B 489
binding site for Di-peptide ILE D 74 and CSD D 75
binding site for Di-peptide CSD D 75 and GLY D 76
binding site for residues H2S D 503 and SEC D 489
binding site for Di-peptide ILE F 74 and CSD F 75
binding site for Di-peptide CSD F 75 and GLY F 76
binding site for residues H2S F 503 and SEC F 489
binding site for Di-peptide ILE H 74 and OCS H 75
binding site for Di-peptide OCS H 75 and GLY H 76
binding site for residues H2S H 503 and SEC H 489
The analyses of the Patterson function reveals a significant off-origin peak that is 56.30 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 2.7936e-05. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.
20191225.v01 (using entries in the PDB archive December 25th 2019)
structure factor analysis and validation
geometric validation package for ligand chemistry in protein x-ray structures