wwPDB validation report of PDB entry 6TKO

Initial placement was done manually in Coot, followed by rigid-body refinement in PHENIX and jelly-body refinement in REFMAC5. Manual remodeling was performed in Coot and iterated with real space refinement in PHENIX. Chemical restraints for formoterol were calculated in eLBOW using AM1 optimisation.

Half maps were locally filtered between refinement iterations using SIDESPLITTER, an adaptation of the LAFTER algorithm that maintains gold-standard separation between the two half maps.

Formoterol-bound beta1-adrenoceptor coupled to beta-arrestin-1 stabilised by Fab30.

Data collected with a stage-tilt of 30deg; two non-overlapping exposures per hole and multi-hole image-shift data acquisition strategies (3x3 holes per stage shift).

Data collected with a stage-tilt of 30deg; two non-overlapping exposures per hole using image-shift.

Blotted for 2-3 seconds before plunging. Liquid ethane maintained at 92.15 K.

Relative to wild-type sequence: construct is truncated at the N-terminus; and in ICL3; its C-terminus is truncated at C358A and fused with a linker to a series of phosphorylated residues (ARGRPLPETGGGDE[pS]A[pT][pT]A[pS][pS][pS]LAKDTSS).

Additional N-terminal Gly residue, in place of starting Met, remaining from proteolytic cleavage.

6IBL contains the same agonist-bound receptor complexed with nanobody Nb80.

Phosphorylated turkey beta1 adrenoceptor with bound agonist formoterol coupled to arrestin-2 in lipid nanodisc.

Beta-1 adrenergic receptor, Beta-arrestin-1, Fab30 heavy chain, Fab30 light chain

binding site for Di-peptide GLU A 1356 and SEP A 1357

binding site for Di-peptide SEP A 1357 and ALA A 1358

binding site for Di-peptide ALA A 1358 and TPO A 1359

binding site for residues TPO A 1359 and TPO A 1360

binding site for Di-peptide TPO A 1360 and ALA A 1361

binding site for Di-peptide ALA A 1361 and SEP A 1362

binding site for residues SEP A 1362 and SEP A 1363

binding site for residues SEP A 1363 and SEP A 1364

binding site for Di-peptide SEP A 1364 and LEU A 1365

Calculated fsc threesigma indicator curve
Author provided fsc threesigma indicator curve
Author provided fsc halfbit indicator curve
Author provided fsc onebit indicator curve
Author provided fsc 0.333 indicator curve
Author provided fsc 0.143 indicator curve
geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)