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. 2016 Oct 22;29(11):477–484. doi: 10.1093/protein/gzw028

Table IV.

Crystal packing effects at the CDR-H3 loops in the X-ray crystal structures

Target (PDBID) Lengtha Crystal packing effectb Resolution (Å) Backbone average B-factor (Å2)c All atoms average B-factor (Å2)d
Ab01 (4ma3) 10 SB between ArgH95sc and GluH1sc 2.00 25.0 28.5
Ab02 (4kuz) 13

  • SB between AspH100sc and ArgH103sc;

  • HB between ArgH103sc and AspH31sc

 2.70 23.4 24.3
Ab03 (4kq3) 10

  • SB between GluH101sc and ArgL210sc;

  • HB between TyrH102sc and carbonyl of ArgL210bb;

  • HB between carbonyl of GluH101bb and LysL189sc

 1.92 23.7 28.1
Ab04 (4kq4) 10 SB between ArgH101sc and GluH10sc 2.45 82.9e 91.2e
Ab05 (4m6m) 10 (No contact) 2.00 25.2 33.4
Ab06 (4m6o) 16

  • SB between AspH108sc and ArgH30sc;

  • HB between TyrH100sc and carbonyl of HisH228bb;

  • HB between HisH105sc and HisH227sc

 2.80 48.1 47.2
Ab07 (4mau) 10

  • SB between AspH100sc and LysH214sc;

  • SB between AspH105sc and LysH214sc

 1.90 24.0 25.6
Ab08 (4m7k) 13 HB between TyrH102sc and carbonyl of LysL194bb 1.90 25.9 29.3
Ab09 (4kmt) 12 (No contact) 2.10 27.7 34.6
Ab10 (4m61) 13

  • SB between ArgH98sc in chain B and LysH50sc in chain D across a sulfate ion (this study)

  • SB between ArgH98sc in chain D and HisL189sc in chain A across a sulfate ion (this study)

 1.62

  • 24.7 (chain B)

  • 15.4 (chain D)

  • 27.6 (chain B)

  • 19.4 (chain D)
Ab11 (4m43) 12

  • HB between AspH98bb and SerL122sc;

  • Van der Waals contact between AspH98bb and SerL122sc

 1.85 14.4 17.2

aLength of the CDR-H3 represented by the number of residues.

bSB, salt bridge and HB, hydrogen bond between the residue in the CDR-H3 loop and the residue in the other neighboring unit cell. sc indicates a side chain, and bb is a backbone. The residue numbers are those in the PDB files, except for the current study for Ab10.

cTemperature factor of the backbone heavy atoms averaged for each CDR-H3 loop, where N- and C-terminal 2 residues at the base were not counted.

dTemperature factor of the all heavy atoms averaged for each CDR-H3 loop, where N- and C-terminal 2 residues at the base were not counted.

eTemperature factors of the entire chains in this PDB entry (4kq4) are all very large by an unknown reason.