wwPDB validation report of PDB entry 5JNF

Crystal structure of the LgrA initiation module excluding the Asub domain: F-A-delta-sub

(chain A and (resseq 2 or (resid 3 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 4:12 or resseq 14:15 or (resid 16 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 17:18 or (resid 19 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 20:33 or (resid 34 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 35:51 or (resid 52 and (name N or name CA or name C or name CB or name H or name HA or name HB1 or name HB2 or name HB3)) or resseq 53:55 or resseq 57:65 or resseq 67:80 or (resid 81 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 82:95 or (resid 96 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 97:108 or (resid 109 and (name N or name CA or name C or name O or name CB or name CG2 or name OG1 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or resseq 110:142 or resseq 144 or resseq 146:149 or (resid 150 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 151:166 or (resid 167 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 168:173 or resseq 175:180 or (resid 181 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resseq 183:195 or resseq 197:198 or (resid 199 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 200:202 or (resid 203 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 204:205 or (resid 206 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 207:210 or resseq 212:214 or resseq 216:231 or resseq 233:242 or (resid 243 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 244:273 or (resid 274 and (name N or name CA or name C or name O or name CB or name CG or name SD or name CE or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or resseq 275:285 or resseq 287:291 or resseq 293:308 or resseq 310:314 or resseq 316:348 or resseq 350 or (resid 358 and (name N or name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid 359 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 360:364 or (resid 365 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or (resid 366 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resseq 367:371 or (resid 372 and (name N or name CA or name C or name O or name CB or name SG or name HB2 or name HB3 or name HG )) or resseq 374:417 or resseq 420:431 or resseq 433:449 or resseq 451 or resseq 453:465 or (resid 467 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 468 or resseq 470:476 or resseq 478:509 or (resid 510 and (name N or name CA or name C or name O )) or resseq 511:514 or resseq 516:522 or (resid 523 and (name N or name CA or name C or name O or name CB or name CG or name CD or name NE2 or name OE1 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resseq 524:550 or resseq 553:564 or resseq 566:568 or resseq 570:582 or (resid 583 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 584:585))

(chain B and (resseq 2 or (resid 3 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 4:12 or resseq 14:51 or (resid 52 and (name N or name CA or name C or name CB or name H or name HA or name HB1 or name HB2 or name HB3)) or resseq 53:55 or resseq 57:65 or resseq 67:95 or (resid 96 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 97:108 or (resid 109 and (name N or name CA or name C or name O or name CB or name CG2 or name OG1 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or resseq 110:142 or resseq 144 or resseq 146:149 or (resid 150 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 151:173 or resseq 175:180 or (resid 181 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resseq 183:195 or resseq 197:202 or (resid 203 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 204:205 or (resid 206 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 207:210 or resseq 212:214 or resseq 216:218 or (resid 219 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resseq 220:231 or resseq 233:242 or (resid 243 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 244:273 or (resid 274 and (name N or name CA or name C or name O or name CB or name CG or name SD or name CE or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or resseq 275:285 or resseq 287:291 or resseq 293:308 or resseq 310:314 or resseq 316:348 or resseq 350 or (resid 358 and (name N or name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid 359 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 360:364 or (resid 365 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or (resid 366 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resseq 367:371 or (resid 372 and (name N or name CA or name C or name O or name CB or name SG or name HB2 or name HB3 or name HG )) or resseq 374:417 or resseq 420:431 or resseq 433:449 or resseq 451 or resseq 453:465 or resseq 467:468 or resseq 470:476 or resseq 478:509 or (resid 510 and (name N or name CA or name C or name O )) or resseq 511:514 or resseq 516:522 or (resid 523 and (name N or name CA or name C or name O or name CB or name CG or name CD or name NE2 or name OE1 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resseq 524:550 or resseq 553:564 or resseq 566:568 or resseq 570:585))

(chain C and (resseq 2 or (resid 3 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 4:12 or resseq 14:15 or (resid 16 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 17:18 or (resid 19 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 20:33 or (resid 34 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 35:51 or (resid 52 and (name N or name CA or name C or name CB or name H or name HA or name HB1 or name HB2 or name HB3)) or resseq 53:55 or resseq 57:65 or resseq 67:80 or (resid 81 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 82:95 or (resid 96 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 97:108 or (resid 109 and (name N or name CA or name C or name O or name CB or name CG2 or name OG1 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or resseq 110:142 or resseq 144 or resseq 146:149 or (resid 150 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 151:166 or (resid 167 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 168:173 or resseq 175:180 or (resid 181 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resseq 183:195 or resseq 197:198 or (resid 199 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 200:202 or (resid 203 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 204:205 or (resid 206 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 207:210 or resseq 212:214 or resseq 216:218 or (resid 219 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resseq 220:231 or resseq 233:242 or (resid 243 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 244:273 or (resid 274 and (name N or name CA or name C or name O or name CB or name CG or name SD or name CE or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or resseq 275:285 or resseq 287:291 or resseq 293:308 or resseq 310:314 or resseq 316:348 or resseq 350 or (resid 358 and (name N or name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or (resid 359 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 360:364 or (resid 365 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or (resid 366 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resseq 367:371 or (resid 372 and (name N or name CA or name C or name O or name CB or name SG or name HB2 or name HB3 or name HG )) or resseq 374:417 or resseq 420:431 or resseq 433:449 or resseq 451 or resseq 453:465 or (resid 467 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 468 or resseq 470:476 or resseq 478:509 or (resid 510 and (name N or name CA or name C or name O )) or resseq 511:514 or resseq 516:522 or (resid 523 and (name N or name CA or name C or name O or name CB or name CG or name CD or name NE2 or name OE1 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resseq 524:550 or resseq 553:564 or resseq 566:568 or resseq 570:582 or (resid 583 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 584:585))

(chain D and (resseq 2:12 or resseq 14:15 or (resid 16 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 17:18 or (resid 19 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 20:33 or (resid 34 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 35:51 or (resid 52 and (name O or name N or name CA or name C or name CB or name H or name HA or name HB1 or name HB2)) or resseq 53:55 or resseq 57:65 or resseq 67:108 or (resid 109 and (name N or name CA or name C or name O or name CB or name CG2 or name OG1 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or resseq 110:142 or resseq 144 or resseq 146:149 or (resid 150 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 151:173 or resseq 175:180 or (resid 181 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resseq 183:195 or resseq 197:205 or (resid 206 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 207:210 or resseq 212:214 or resseq 216:231 or resseq 233:242 or (resid 243 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resseq 244:273 or (resid 274 and (name N or name CA or name C or name O or name CB or name CG or name SD or name CE or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or resseq 275:285 or resseq 287:291 or resseq 293:308 or resseq 310:314 or resseq 316:348 or resseq 350 or resseq 358:364 or (resid 365 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or (resid 366 and (name N or name CA or name C or name O or name CB or name CG or name CD2 or name ND1 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resseq 367:371 or (resid 372 and (name N or name CA or name C or name O or name CB or name SG or name HB2 or name HB3 or name HG )) or resseq 374:417 or resseq 420:431 or resseq 433:449 or resseq 451 or resseq 453:465 or resseq 467:468 or resseq 470:476 or resseq 478:509 or (resid 510 and (name N or name CA or name C or name O )) or resseq 511:514 or resseq 516:522 or (resid 523 and (name N or name CA or name C or name O or name CB or name CG or name CD or name NE2 or name OE1 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resseq 524:550 or resseq 553:564 or resseq 566:568 or resseq 570:582 or (resid 583 and (name N or name CA or name C or name O or name CB or name H or name HA )) or resseq 584:585))

The analyses of the Patterson function reveals a significant off-origin peak that is 37.19 % 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 4.4522e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details.

structure factor analysis and validation
geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)