scholarly journals A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures

2021 ◽  
Vol 77 (4) ◽  
Author(s):  
Jordi Rius ◽  
Xavier Torrelles
Keyword(s):  
Crystal Structures ◽  
Random Phase ◽  
Data Bank ◽  
Atomic Resolution ◽  
Modulus Function ◽  
Type Synthesis ◽  
Acta Cryst ◽  
Modification Procedure ◽  
Cl Atoms ◽  
Resolution Data

The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489–493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.

Use of Patterson-based methods automatically to determine the structures of heavy-atom-containing proteins with up to 6000 non-hydrogen atoms in the asymmetric unit

2006 ◽  
Vol 39 (5) ◽  
pp. 728-734 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Heavy Atom ◽  
Data Bank ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Heavy Atoms ◽  
Density Maps ◽  
Resolution Data

The Patterson superposition methods described by Burlaet al.[J. Appl. Cryst.(2006),39, 527–535], based on the use of the `multiple implication functions', have been enriched by supplementary filtering techniques based on some general (resolution-dependent) features of both the Patterson and the electron density maps. The method has been implemented in a modified version of the programSIR2004and tested using a set of 20 crystal structures selected from the Protein Data Bank, having a number of non-hydrogen atoms in the asymmetric unit larger than 2000, atomic resolution data and some heavy atoms (equal to or heavier than Ca). The new phasing procedure is able to solve most of the test structures, among which there are two proteins with more than 6000 non-hydrogen atoms in the asymmetric unit, so extending by far the complexity today commonly considered as the limit for Patterson-based methods (i.e.about 2000 non-hydrogen atoms).

scholarly journals Crystal structures of tris[1-oxopyridine-2-olato(1−)]silicon(IV) chloride chloroform-d1disolvate, tris[1-oxopyridine-2-olato(1−)]silicon(IV) chloride acetonitrile unquantified solvate, andfac-tris[1-oxopyridine-2-thiolato(1−)]silicon(IV) chloride chloroform-d1disolvate

2015 ◽  
Vol 71 (12) ◽  
pp. 1531-1535 ◽  
Author(s):  
Bradley M. Kraft ◽  
William W. Brennessel ◽  
Amy E. Ryan ◽  
Candace K. Benjamin
Keyword(s):  
Crystal Structures ◽  
Unit Cell ◽  
The Other ◽  
Acta Cryst ◽  
Distorted Octahedral Coordination ◽  
Structure Factors ◽  
Distorted Octahedral ◽  
Coordination Spheres ◽  
Van Der Waals Radii ◽  
Cl Atoms

The cations in the title salts, [Si(OPO)3]Cl·2CDCl3, (I), [Si(OPO)3]Cl·xCH3CN, (II), andfac-[Si(OPTO)3]Cl·2CDCl3, (III) (OPO = 1-oxo-2-pyridinone, C5H4NO2, and OPTO = 1-oxo-2-pyridinethione, C5H4NOS), have distorted octahedral coordination spheres. The first two structures contain the same cation and anion, but different solvents of crystallization led to different solvates and packing arrangements. In structures (I) and (III), the silicon complex cations and chloride anions are well separated, while in (II), there are two C—H...Cl distances that fall just within the sum of the van der Waals radii of the C and Cl atoms. The pyridine portions of the OPO ligands in (I) and (II) are modeled as disordered with the planar flips of themselves [(I): 0.574 (15):0.426 (15), 0.696 (15):0.304 (15), and 0.621 (15):0.379 (15); (II): 0.555 (13):0.445 (13), 0.604 (14):0.396 (14) and 0.611 (13):0.389 (13)], demonstrating that bothfacandmerisomers are co-crystallized. In (II), highly disordered solvent, located in two independent channels along [100], was unable to be modeled. Reflection contributions from this solvent were fixed and added to the calculated structure factors using the SQUEEZE [Spek (2015).Acta Cryst.C71, 9–18] function of programPLATON, which determined there to be 54 electrons in 225 Å3accounted for per unit cell (25 electrons in 109 Å3in one channel, and 29 electrons in 115 Å3in the other). In (I) and (II), all species lie on general positions. In (III), all species are located along crystallographic threefold axes.

The revenge of the Patterson methods. I. Proteinab initiophasing

2006 ◽  
Vol 39 (4) ◽  
pp. 527-535 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Computing Time ◽  
Direct Methods ◽  
Data Bank ◽  
Atomic Resolution ◽  
Atomic Data ◽  
Large Set ◽  
Hydrogen Atoms ◽  
Data Resolution ◽  
Structure Complexity

Direct methods combined with direct-space refinement procedures are the standard tools forab initiocrystal structure solution of macromoleculesviadiffraction data collected up to atomic or quasi-atomic resolution. An entirely direct-space approach is described here: it includes an automated Patterson deconvolution method, based on the minimum superposition function, followed by an effective direct-space refinement, consisting of cycles of electron density modification. The new approach has been implemented in a new version of theSIR2004program and tested on a large set of test structures selected from the Protein Data Bank, with data resolution better than 1.6 Å and number of non-hydrogen atoms in the asymmetric unit up to 2000. The new procedure proved to be extremely efficient and very fast in solving crystal structures with atomic resolution data and heavy atoms: their solution and refinement requires a computing time roughly comparable with that necessary for solving small-molecule crystal structuresviaa modern computer program. It markedly overcomes direct methods, even for crystal structures with atomic data resolution and heaviest atomic species up to calcium, as well as for crystal structures with quasi-atomic data resolution (i.e.1.2–1.6 Å). The Patterson approach proved to be loosely dependent on the structure complexity.

scholarly journals Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

2021 ◽  
Vol 18 (2) ◽  
pp. 156-164 ◽  
Author(s):  
Catherine L. Lawson ◽  
Andriy Kryshtafovych ◽  
Paul D. Adams ◽  
Pavel V. Afonine ◽  
Matthew L. Baker ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structure Data ◽  
Model Evaluation ◽  
Data Bank ◽  
High Accuracy ◽  
Atomic Resolution ◽  
Software Developers ◽  
Data Archives ◽  
Modeling Software

AbstractThis paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir

2007 ◽  
Vol 67 (1) ◽  
pp. 232-242 ◽  
Author(s):  
Yunfeng Tie ◽  
Andrey Y. Kovalevsky ◽  
Peter Boross ◽  
Yuan-Fang Wang ◽  
Arun K. Ghosh ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Atomic Resolution ◽  
Hiv 1

scholarly journals Validation and correction of Zn–Cys x His y complexes

2016 ◽  
Vol 72 (10) ◽  
pp. 1110-1118 ◽  
Author(s):  
Wouter G. Touw ◽  
Bart van Beusekom ◽  
Jochem M. G. Evers ◽  
Gert Vriend ◽  
Robbie P. Joosten
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Model Validation ◽  
Data Bank ◽  
Zinc Complexes ◽  
Zinc Ions ◽  
Tetrahedral Complex ◽  
Context Sensitive

Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn–Cys distances and Cys–Zn–Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.

Three new phosphoric triamides with a [C(O)NH]P(O)[N(C)(C)]2skeleton: a database analysis of C—N—C and P—N—C bond angles

2014 ◽  
Vol 70 (10) ◽  
pp. 998-1002 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Arnold L. Rheingold ◽  
James A. Golen
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Database Analysis ◽  
Acta Cryst ◽  
Bond Angles ◽  
Cyclic Amide ◽  
Phosphoric Triamide ◽  
Structural Database ◽  
Phosphoric Triamides

InN,N,N′,N′-tetraethyl-N′′-(4-fluorobenzoyl)phosphoric triamide, C15H25FN3O2P, (I), andN-(2,6-difluorobenzoyl)-N′,N′′-bis(4-methylpiperidin-1-yl)phosphoric triamide, C19H28F2N3O2P, (II), the C—N—C angle at each tertiary N atom is significantly smaller than the two P—N—C angles. For the other new structure,N,N′-dicyclohexyl-N′′-(2-fluorobenzoyl)-N,N′-dimethylphosphoric triamide, C21H33FN3O2P, (III), one C—N—C angle [117.08 (12)°] has a greater value than the related P—N—C angle [115.59 (9)°] at the same N atom. Furthermore, for most of the analogous structures with a [C(=O)NH]P(=O)[N(C)(C)]2skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002).Acta Cryst.B58, 380–388], the C—N—C angle is significantly smaller than the two P—N—C angles; exceptions were found for four structures with theN-methylcyclohexylamide substituent, similar to (III), one structure with the seven-membered cyclic amide azepan-1-yl substituent and one structure with anN-methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linkedviapairs of N—H...O=P hydrogen bonds to form dimers.

FINDNCS: a program to detect non-crystallographic symmetries in protein crystals from heavy-atom sites

1999 ◽  
Vol 32 (2) ◽  
pp. 365-368 ◽  
Author(s):  
Guoguang Lu
Keyword(s):  
Protein Data Bank ◽  
Root Mean Square ◽  
Heavy Atom ◽  
Data Bank ◽  
Protein Crystals ◽  
Translation Vector ◽  
Mean Square ◽  
Acta Cryst ◽  
Crystallographic Symmetry ◽  
Averaging Techniques

In order to facilitate applications of averaging techniques in the MIR/MAD procedure, a program,FINDNCS, which automatically identifies non-crystallographic symmetry (NCS) from heavy-atom sites, has been developed. The program outputs the NCS operations (a rotation matrix and a translation vector), the corresponding root-mean-square (r.m.s.) deviations of heavy-atom sites, polar angles and screw translations, and writes coordinates of matching sites in Protein Data Bank (PDB) format. The program has an interface with the graphics programO[Joneset al. (1991).Acta Cryst.A47, 110–119] so that the NCS operations can be displayed automatically. In the test examples, all the correct NCS operations were identified and were above the noise solutions.

scholarly journals Accurate geometrical restraints for Watson–Crick base pairs

2019 ◽  
Vol 75 (2) ◽  
pp. 235-245 ◽  
Author(s):  
Miroslaw Gilski ◽  
Jianbo Zhao ◽  
Marcin Kowiel ◽  
Dariusz Brzezinski ◽  
Douglas H. Turner ◽  
...  
Keyword(s):  
Structural Information ◽  
Data Bank ◽  
Base Pairs ◽  
Acta Cryst ◽  
Ultrahigh Resolution ◽  
Cryo Electron Microscopy ◽  
Structural Database ◽  
Different Sources ◽  
Best Parameters

Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.

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