scholarly journals The solvent component of macromolecular crystals

2015 ◽  
Vol 71 (5) ◽  
pp. 1023-1038 ◽  
Author(s):  
Christian X. Weichenberger ◽  
Pavel V. Afonine ◽  
Katherine Kantardjieff ◽  
Bernhard Rupp
Keyword(s):  
Crystal Structure ◽  
Small Molecule ◽  
Mother Liquor ◽  
Structure Refinement ◽  
Solvent Models ◽  
Solvent Model ◽  
Solvent Density ◽  
Small Molecule Ligands ◽  
Solvent Component ◽  
Atomic Crystal

The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.

scholarly journals Improved ligand geometries in crystallographic refinement usingAFITTinPHENIX

2016 ◽  
Vol 72 (9) ◽  
pp. 1062-1072 ◽  
Author(s):  
Pawel A. Janowski ◽  
Nigel W. Moriarty ◽  
Brian P. Kelley ◽  
David A. Case ◽  
Darrin M. York ◽  
...  
Keyword(s):  
Small Molecule ◽  
Structure Refinement ◽  
Difficult Problem ◽  
Amino Acid Residues ◽  
Data Set ◽  
Fully Integrated ◽  
Chemical Complexity ◽  
Parameter Ratio ◽  
Small Molecule Ligands ◽  
Multiple Ligands

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.PHENIX–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows.PHENIX–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.

Iron in kornerupine; a57Fe Moessbauer spectroscopic study and comparison with single-crystal structure refinement

1999 ◽  
Vol 84 (4) ◽  
pp. 536-549 ◽  
Author(s):  
Edward S. Grew ◽  
Guenther J. Redhammer ◽  
Georg Amthauer ◽  
Mark A. Cooper ◽  
Frank C. Hawthorne ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Spectroscopic Study ◽  
Structure Refinement ◽  
Single Crystal Structure ◽  
Crystal Structure Refinement

scholarly journals Allergens and their associated small molecule ligands ‐ their dual role in sensitization

Allergy ◽  
2021 ◽  
Author(s):  
Maksymilian Chruszcz ◽  
Fook Tim Chew ◽  
Karin Hoffmann‐Sommergruber ◽  
Barry K. Hurlburt ◽  
Geoffrey A. Mueller ◽  
...  
Keyword(s):  
Small Molecule ◽  
Dual Role ◽  
Small Molecule Ligands

scholarly journals Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate

2015 ◽  
Vol 71 (2) ◽  
pp. 199-205 ◽  
Author(s):  
George T. Lountos ◽  
Scott Cherry ◽  
Joseph E. Tropea ◽  
David S. Waugh
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Phosphatase Activity ◽  
Small Molecule ◽  
Molecular Basis ◽  
Protein Tyrosine Phosphatases ◽  
Simple Method ◽  
Dual Specificity Phosphatase ◽  
Dual Specificity ◽  
Nitrophenyl Phosphate

4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in complex with pNPP. The structure illuminates the molecular basis for substrate binding and may also facilitate the structure-assisted development of DUSP22 inhibitors.

The crystal chemistry of the uranyl carbonate mineral grimselite, (K, Na)3Na[(UO2)(CO3)3](H2O), from Jáchymov, Czech Republic

2012 ◽  
Vol 76 (3) ◽  
pp. 443-453 ◽  
Author(s):  
J. Plášil ◽  
K. Fejfarová ◽  
R. Skála ◽  
R. Škoda ◽  
N. Meisser ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Czech Republic ◽  
Structure Refinement ◽  
Unit Cell ◽  
Carbonate Mineral ◽  
X Ray Diffraction ◽  
The Czech Republic ◽  
Cell Parameters ◽  
Uranyl Carbonate ◽  
Diffraction Peaks

AbstractTwo crystals of the uranyl carbonate mineral grimselite, ideally K3Na[(UO2)(CO3)3](H2O), from Jáchymov in the Czech Republic were studied by single-crystal X-ray diffraction and electron-probe microanalysis. One crystal has considerably more Na than the ideal chemical composition due to substitution of Na into KO8 polyhedra; the composition of the other crystal is nearer to ideal, and similar to synthetic grimselite. The presence of Na atoms in KO8 polyhedra, which are located in channels in the crystal structure, reduces their volume, and as a result the unit-cell volume also decreases. Structure refinement shows that the formula for the sample with the anomalously high Na content is (K2.43Na0.57)Σ3.00Na[(UO2)(CO3)3](H2O). The unit-cell parameters, refined in space group P2c, are a = 9.2507(1), c = 8.1788(1) Å, V = 606.14(3) Å3 and Z = 2. The crystal structure was refined to R1 = 0.0082 and wR1 = 0.0185 with a GOF = 1.33, based on 626 observed diffraction peaks [Iobs>3σ(I)].

Sign in / Sign up

Export Citation Format

Share Document