Phenix/DivCon

Protein crystallography plays a critical role in structure-aided drug design, however crystallographic refinement at moderate resolution relies heavily on stereochemical restraints including atom types, bond configurations, and so on to ensure the correct model. To overcome conventional refinement limitations, we have replaced these fixed empirical stereochemistry restraints in Phenix with data determined through rigorous quantum mechanical treatment of the complex in real-time. See the examples below of several recently completed refinements of PDB structures.

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Overall view of the PDB structure 1MRL

Downloads: PDB File MTZ File

PDB Details:

PDB ID: 1MRL
PDB Title: Crystal Structure of Streptogramin A Acetyltransferase with Dalfopristin
Deposition year: 2002
Experimental Method: X-RAY DIFFRACTION
Resolution: 2.8 Å
Space Group: P21 21 21
Unit Cell:
a=82.91α=90.00
b=90.90β=90.00
c=104.53γ=90.00

 Original PDBQM-Refinement
R-work0.2720.232
R-free0.3040.310

Ligand Details:

Ligand ID: DOL (Chain A)
Ligand Formula: C34 H50 N4 O9 S
Ligand Name: 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE

 Original PDBQM-Refinement
Ligand Strain Energy (PM6 Kcal/Mole)667.1757.78

The electron density 2Fo-Fc around the ligand in the structure 1MRL re-refined with the QM protocol (green) and superimposed with the original PDB ligand (yellow). The map is contoured at 1s.

The ligand in the structure 1MRL re-refined with the QM protocol (green) and superimposed with the original PDB ligand (yellow).

Overall view of the PDB structure 2CJU

Downloads: PDB File MTZ File

PDB Details:

PDB ID: 2CJU
PDB Title: Crystal Structure Of The Tepc15-Vk45.1 Anti-2-Phenyl-5-Oxazolone NQ16-113.8 SCFV in Complex with Phoxgaba
Deposition year: 2006
Experimental Method: X-RAY DIFFRACTION
Resolution: 2.5 Å
Space Group: I 21 21 21
Unit Cell:
a=51.97α=90.00
b=74.19β=90.00
c=134.18γ=90.00

 Original PDBQM-Refinement
R-work0.2410.216
R-free0.2910.300

Ligand Details:

Ligand ID: PHX
Ligand Formula: C14 H12 N2 O4
Ligand Name: 4-{[(Z)-(5-OXO-2-PHENYL-1,3-OXAZOL-4(5H)-YLIDENE)METHYL]AMINO}BUTANOIC ACID

 Original PDBQM-Refinement
Ligand Strain Energy (PM6 Kcal/Mole)557.5816.85

The electron density 2Fo-Fc around the ligand in the structure 2CJU re-refined with the QM protocol (green) and superimposed with the original PDB ligand (yellow). The map is contoured at 1s.

The ligand in the structure 2CJU re-refined with the QM protocol (green) and superimposed with the original PDB ligand (yellow).

Overall view of the PDB structure 2JK7

Downloads: PDB File MTZ File

PDB Details:

PDB ID: 2JK7
PDB Title: XIAP BIR3 Bound to a SMAC Mimetic
Deposition year: 2008
Experimental Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
Space Group: P 65 2 2
Unit Cell:
a=115.76α=90.00
b=115.76β=90.00
c=61.79γ=120.00

 Original PDBQM-Refinement
R-work0.2290.214
R-free0.2760.263

Ligand Details:

Ligand ID: BI6
Ligand Formula: C36 H34 N4 O3 S
Ligand Name: (3S,6S,7Z,10AS)-N-(DIPHENYLMETHYL)-6-{[(2S)-2
-(METHYLIDENEAMINO)BUTANOYL]AMINO}-5-OXO-1,2,3,5,6,9,10,10
A-OCTAHYDROPYRROLO[1,2-A]AZOCINE-3-CARBOXAMIDE

 Original PDBQM-Refinement
Ligand Strain Energy (PM6 Kcal/Mole)260.0335.46

The electron density 2Fo-Fc around the ligand in the structure 2JK7 re-refined with the QM protocol (green) and superimposed with the original PDB ligand (yellow). The map is contoured at 1s.

The ligand in the structure 2JK7 re-refined with the QM protocol (green) and superimposed with the original PDB ligand (yellow).