wwPDB validation report of PDB entry 2RTB

THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE
REFINED:
ALA B 13
GLU B 14
ALA B 15
GLU B 51 (CG, HG1, HG2, CD, OE1, OE2)
ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22)
ARG B 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22)
GLY B 98
GLY B 99
ALA B 100
GLU B 101
ALA B 102
ARG B 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22)
GLU B 116 (CG, HG1, HG2, CD, OE1, OE2)
LYS B 134
PRO B 135
ALA D 13
GLU D 14
ALA D 15
ASP D 36 (CG, OD1, OD2)
ARG D 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22)
ASN D 82 (CG, OD1, ND2, HD21, HD22)
ARG D 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22)
ALA D 100
GLU D 101 (CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2)
ARG D 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22)
GLU D 116 (CG, HG1, HG2, CD, OE1, OE2)
VAL D 133

RESIDUES TYR B 60 THROUGH SER B 69 AND TYR D 60 THROUGH
SER D 69 WERE REFINED IN TWO CONFORMATIONS BECAUSE UPON
PROTONATION OF ASP 61 AT LOW PH, ASP 61 UNDERGOES A LARGE
SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE
LOOPS COMPRISING RESIDUES ASP B 61 THROUGH SER B 69 AND
ASP D 61 THROUGH SER D 69 ALSO UNDERGO CORRESPONDING
CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE
DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION.

TYR B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH
OCCUPIES A SIMILAR REGION OF SPACE AS A 2-FOLD RELATED
B 22. PROPER REFINEMENT WITH XPLOR IS NOT POSSIBLE BECAUSE
OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY RELATED
COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR
DENSITY DUE TO THIS CONFORMER OF TYR B 22: HOH 491,
HOH 1460. NO HYDROGENS ARE INCLUDED FOR THESE "WATERS".

APOSTREPTAVIDIN, PH 3.32, SPACE GROUP I222

The largest off-origin peak in the Patterson function is 9.87% of the height of the origin peak. No significant pseudotranslation is detected.

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)