Polder maps: Improving OMIT maps by excluding bulk solvent

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; Poon, Billy K.; Sobolev, Oleg V.; Terwilliger, Thomas Charles; Adams, Paul D.

doi:10.1107/S2059798316018210

Title: Polder maps: Improving OMIT maps by excluding bulk solvent

Journal Article · Wed Feb 01 04:00:00 UTC 2017 · Acta Crystallographica. Section D. Structural Biology

DOI: https://doi.org/10.1107/S2059798316018210 · OSTI ID:1344357

Liebschner, Dorothee ^[1]; Afonine, Pavel V. ^[1]; Moriarty, Nigel W. ^[1]; Poon, Billy K. ^[1]; Sobolev, Oleg V. ^[1];

^[2]; Adams, Paul D. ^[3]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.

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Research Organization:: Los Alamos National Laboratory (LANL)

Sponsoring Organization:: National Institutes of Health; USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1344357

Report Number(s):: LA-UR--16-24457

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Issue: 2 Vol. 73; ISSN 2059-7983; ISSN ACSDAD

Publisher:: IUCrCopyright Statement

Country of Publication:: United States

Language:: English

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Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase González, Javier M.; Marti-Arbona, Ricardo; Chen, Julian C. -H. Acta Crystallographica Section F Structural Biology Communications, Vol. 74, Issue 10 https://doi.org/10.1107/s2053230x18011809	journal	September 2018
Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic sulfur-oxidizing bacterium Thioalkalivibrio paradoxus ARh 1 Osipov, Eugeny M.; Lilina, Anastasia V.; Tsallagov, Stanislav I. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 7 https://doi.org/10.1107/s2059798318005648	journal	June 2018
Precipitant–ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase Thompson, Andrew P.; Wegener, Kate L.; Booker, Grant W. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 10 https://doi.org/10.1107/s2059798318010136	journal	October 2018
Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography Keedy, Daniel A. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 2 https://doi.org/10.1107/s2059798318017941	journal	January 2019
Crystal structures of the naturally fused CS and cytochrome b 5 reductase ( b 5 R) domains of Ncb5or reveal an expanded CS fold, extensive CS– b 5 R interactions and productive binding of the NAD(P) + nicotinamide ring Benson, David R.; Lovell, Scott; Mehzabeen, Nurjahan Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 7 https://doi.org/10.1107/s205979831900754x	journal	June 2019
Crystal structures of the naturally fused CS and cytochrome b ₅ reductase ( b ₅ R) domains of Ncb5or reveal an expanded CS fold, extensive CS– b ₅ R interactions and productive binding of the NAD(P) ⁺ nicotinamide ring Benson, David R.; Lovell, Scott; Mehzabeen, Nurjahan International Union of Crystallography (IUCr) https://doi.org/10.1107/s205979831900754x/dw5198sup1.pdf	text	January 2019
Comparison of a retroviral protease in monomeric and dimeric states Wosicki, Stanislaw; Gilski, Miroslaw; Zabranska, Helena Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/s2059798319011355	journal	September 2019
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/s2059798319011471	journal	October 2019
Well-based crystallization of lipidic cubic phase microcrystals for serial X-ray crystallography experiments Andersson, Rebecka; Safari, Cecilia; Båth, Petra Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/s2059798319012695	journal	October 2019
Crystal structure of rhodopsin in complex with a mini-G _o sheds light on the principles of G protein selectivity Tsai, Ching-Ju; Pamula, Filip; Nehmé, Rony Science Advances, Vol. 4, Issue 9 https://doi.org/10.1126/sciadv.aat7052	journal	September 2018
Mechanism of β ₂ AR regulation by an intracellular positive allosteric modulator Liu, Xiangyu; Masoudi, Ali; Kahsai, Alem W. Science, Vol. 364, Issue 6447 https://doi.org/10.1126/science.aaw8981	journal	June 2019
Time-resolved crystallography reveals allosteric communication aligned with molecular breathing Mehrabi, Pedram; Schulz, Eike C.; Dsouza, Raison Science, Vol. 365, Issue 6458 https://doi.org/10.1126/science.aaw9904	journal	September 2019
The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria Zhang, Heng; Burrows, Judith; Card, Graeme L. PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0206709	journal	April 2019
An oligomeric state‐dependent switch in the ER enzyme FICD regulates AMP ylation and de AMP ylation of BiP Perera, Luke A.; Rato, Claudia; Yan, Yahui The EMBO Journal, Vol. 38, Issue 21 https://doi.org/10.15252/embj.2019102177	journal	September 2019
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43042	text	January 2019
An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP. Perera, Luke; Rato, Claudia; Yan, Yahui Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43330	text	January 2019
Effects of Proline Substitutions on the Thermostable LOV Domain from Chloroflexus aggregans Remeeva, Alina; Nazarenko, Vera V.; Goncharov, Ivan M. RWTH Aachen University https://doi.org/10.18154/rwth-2020-05974	text	January 2020
Molecular mechanism of light-driven sodium pumping Kovalev, Kirill; Astashkin, Roman; Gushchin, Ivan RWTH Aachen University https://doi.org/10.18154/rwth-2020-07237	text	January 2020
Asymmetric activation mechanism of a homodimeric red light-regulated photoreceptor Gourinchas, Geoffrey; Heintz, Udo; Winkler, Andreas Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2018-02520	text	January 2018
The hit-and-return system enables efficient time-resolved serial synchrotron crystallography Schulz, Eike C.; Mehrabi, Pedram; Müller-Werkmeister, Henrike M. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2019-00026	text	January 2018
Molecular mechanism of light-driven sodium pumping Kovalev, Kirill; Astashkin, Roman; Gushchin, Ivan Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2020-03192	text	January 2020
Effects of Proline Substitutions on the Thermostable LOV Domain from Chloroflexus aggregans Remeeva, Alina; Nazarenko, Vera V.; Goncharov, Ivan M. Crystals, Vol. 10, Issue 4 https://doi.org/10.3390/cryst10040256	journal	March 2020
The Structure of Sucrose-Soaked Levansucrase Crystals from Erwinia tasmaniensis reveals a Binding Pocket for Levanbiose Polsinelli, Ivan; Caliandro, Rosanna; Demitri, Nicola International Journal of Molecular Sciences, Vol. 21, Issue 1 https://doi.org/10.3390/ijms21010083	journal	December 2019
Increasing Polarity in Tacrine and Huprine Derivatives: Potent Anticholinesterase Agents for the Treatment of Myasthenia Gravis Galdeano, Carles; Coquelle, Nicolas; Cieslikiewicz-Bouet, Monika Molecules, Vol. 23, Issue 3 https://doi.org/10.3390/molecules23030634	journal	March 2018
Structural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody Perez, Camilo; Köhler, Martin; Janser, Daniel ETH Zurich https://doi.org/10.3929/ethz-b-000233731	text	January 2017
Crystal structure of rhodopsin in complex with a mini-Go sheds light on the principles of G protein selectivity Ching-Ju, Tsai,; Filip, Pamula,; Rony, Nehmé, ETH Zurich https://doi.org/10.3929/ethz-b-000295633	text	January 2018
Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR Niranjan, Varma,; Eshita, Mutt,; Jonas, Mühle, ETH Zurich https://doi.org/10.3929/ethz-b-000352552	text	January 2019
Asymmetric activation mechanism of a homodimeric red light-regulated photoreceptor Gourinchas, Geoffrey; Heintz, Udo; Winkler, Andreas eLife, Vol. 7 https://doi.org/10.7554/eLife.34815	journal	June 2018
Structural basis of ribosomal peptide macrocyclization in plants Haywood, Joel; Schmidberger, Jason W.; James, Amy M. eLife, Vol. 7 https://doi.org/10.7554/elife.32955	journal	January 2018
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering Keedy, Daniel A.; Hill, Zachary B.; Biel, Justin T. eLife, Vol. 7 https://doi.org/10.7554/elife.36307	journal	June 2018

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