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Title: Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

Abstract

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.

Authors:
 [1];  [1];  [2];  [3]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1421812
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Applied Crystallography (Online)
Additional Journal Information:
Journal Name: Journal of Applied Crystallography (Online); Journal Volume: 50; Journal Issue: 5; Journal ID: ISSN 1600-5767
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; crystallization screens; crystal packing; ions and buffers; crystal growth; structural biology

Citation Formats

Pereira, Jose H., McAndrew, Ryan P., Tomaleri, Giovani P., and Adams, Paul D. Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. United States: N. p., 2017. Web. doi:10.1107/S1600576717011347.
Pereira, Jose H., McAndrew, Ryan P., Tomaleri, Giovani P., & Adams, Paul D. Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. United States. doi:10.1107/S1600576717011347.
Pereira, Jose H., McAndrew, Ryan P., Tomaleri, Giovani P., and Adams, Paul D. Tue . "Berkeley Screen: a set of 96 solutions for general macromolecular crystallization". United States. doi:10.1107/S1600576717011347. https://www.osti.gov/servlets/purl/1421812.
@article{osti_1421812,
title = {Berkeley Screen: a set of 96 solutions for general macromolecular crystallization},
author = {Pereira, Jose H. and McAndrew, Ryan P. and Tomaleri, Giovani P. and Adams, Paul D.},
abstractNote = {Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.},
doi = {10.1107/S1600576717011347},
journal = {Journal of Applied Crystallography (Online)},
number = 5,
volume = 50,
place = {United States},
year = {2017},
month = {9}
}

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Works referenced in this record:

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

Cryo-EM of macromolecular assemblies at near-atomic resolution
journal, September 2010

  • Baker, Matthew L.; Zhang, Junjie; Ludtke, Steven J.
  • Nature Protocols, Vol. 5, Issue 10
  • DOI: 10.1038/nprot.2010.126

The Protein Data Bank
journal, January 2000


De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
journal, May 2016


Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin
journal, February 2016

  • Eudes, Aymerick; Pereira, Jose H.; Yogiswara, Sasha
  • Plant and Cell Physiology, Vol. 57, Issue 3
  • DOI: 10.1093/pcp/pcw016

Computational design of self-assembling cyclic protein homo-oligomers
journal, December 2016

  • Fallas, Jorge A.; Ueda, George; Sheffler, William
  • Nature Chemistry, Vol. 9, Issue 4
  • DOI: 10.1038/nchem.2673

Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin
journal, December 2015

  • Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.
  • Journal of Biological Chemistry, Vol. 291, Issue 10
  • DOI: 10.1074/jbc.M115.694307

Sparse matrix sampling: a screening method for crystallization of proteins
journal, August 1991


Alcohol oxidase, a flavoprotein from several basidiomycetes species
journal, February 1968


Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions
journal, November 2013

  • Javidpour, Pouya; Pereira, Jose H.; Goh, Ee-Been
  • Applied and Environmental Microbiology, Vol. 80, Issue 2
  • DOI: 10.1128/AEM.03194-13

Analysis of crystallization data in the Protein Data Bank
journal, September 2015

  • Kirkwood, Jobie; Hargreaves, David; O'Keefe, Simon
  • Acta Crystallographica Section F Structural Biology Communications, Vol. 71, Issue 10
  • DOI: 10.1107/S2053230X15014892

Magnesium Coordination Controls the Molecular Switch Function of DNA Mismatch Repair Protein MutS
journal, February 2010

  • Lebbink, Joyce H. G.; Fish, Alexander; Reumer, Annet
  • Journal of Biological Chemistry, Vol. 285, Issue 17
  • DOI: 10.1074/jbc.M109.066001

Principles for designing proteins with cavities formed by curved β sheets
journal, January 2017

  • Marcos, Enrique; Basanta, Benjamin; Chidyausiku, Tamuka M.
  • Science, Vol. 355, Issue 6321
  • DOI: 10.1126/science.aah7389

A comparison of salts for the crystallization of macromolecules
journal, February 2001


Introduction to protein crystallization
journal, December 2013

  • McPherson, Alexander; Gavira, Jose A.
  • Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 1
  • DOI: 10.1107/S2053230X13033141

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core
journal, December 2016

  • Mills, Jeremy H.; Sheffler, William; Ener, Maraia E.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 52
  • DOI: 10.1073/pnas.1600188113

Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy
journal, September 2005

  • Newman, Janet; Egan, David; Walter, Thomas S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 10
  • DOI: 10.1107/S0907444905024984

2 .ANG. Resolution Structure of DppA, a Periplasmic Dipeptide Transport/Chemosensory Receptor
journal, December 1995

  • Nickitenko, Alexei V.; Trakhanov, Sergei; Quiocho, Florante A.
  • Biochemistry, Vol. 34, Issue 51
  • DOI: 10.1021/bi00051a006

Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima
journal, December 2010

  • Pereira, Jose H.; Chen, Zhiwei; McAndrew, Ryan P.
  • Journal of Structural Biology, Vol. 172, Issue 3, p. 372-379
  • DOI: 10.1016/j.jsb.2010.06.018

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6
journal, March 2016

  • Pereira, Jose Henrique; Heins, Richard A.; Gall, Daniel L.
  • Journal of Biological Chemistry, Vol. 291, Issue 19
  • DOI: 10.1074/jbc.M115.700427

Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy
journal, June 2017


Structural and Biochemical Studies of Actin in Complex with Synthetic Macrolide Tail Analogues
journal, July 2014

  • Pereira, Jose H.; Petchprayoon, Chutima; Hoepker, Alexander C.
  • ChemMedChem, Vol. 9, Issue 10
  • DOI: 10.1002/cmdc.201402150

Mechanism of nucleotide sensing in group II chaperonins: Nucleotide sensing in group II chaperonins
journal, December 2011

  • Pereira, Jose H.; Ralston, Corie Y.; Douglas, Nicholai R.
  • The EMBO Journal, Vol. 31, Issue 3
  • DOI: 10.1038/emboj.2011.468

Crystal Structures of a Group II Chaperonin Reveal the Open and Closed States Associated with the Protein Folding Cycle
journal, June 2010

  • Pereira, Jose H.; Ralston, Corie Y.; Douglas, Nicholai R.
  • Journal of Biological Chemistry, Vol. 285, Issue 36
  • DOI: 10.1074/jbc.M110.125344

Magnesium homeostasis in mammalian cells
journal, January 2007

  • Romani, Andrea, M. P.
  • Frontiers in Bioscience, Vol. 12, Issue 1
  • DOI: 10.2741/2066

Influence of divalent cations in protein crystallization
journal, September 1995


The Biomolecular Crystallization Database Version 4: expanded content and new features
journal, December 2008

  • Tung, Michael; Gallagher, D. Travis
  • Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 1
  • DOI: 10.1107/S0907444908035440

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Towards atomic resolution structural determination by single-particle cryo-electron microscopy
journal, April 2008