The Crystal Screening Interface at ALS
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The Crystal Screening Interface at ALS Nicholas Sauter, Lawrence Berkeley National Lab Crystallography Beam Line Automation: Work Smarter Not Harder Stanford Synchrotron Radiation Laboratory—30 th Annual Users’ Meeting October 8, 2003 Paul Adams, Computational Crystallography Initiative Thomas Earnest, Berkeley Center for Structural Biology
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The Crystal Screening Interface at ALS. Crystallography Beam Line Automation: Work Smarter Not Harder Stanford Synchrotron Radiation Laboratory—30 th Annual Users’ Meeting October 8, 2003. Nicholas Sauter, Lawrence Berkeley National Lab. Paul Adams, Computational - PowerPoint PPT Presentation
Transcript of The Crystal Screening Interface at ALS
The Crystal Screening Interface at ALS
Nicholas Sauter, Lawrence Berkeley National Lab
Crystallography Beam Line Automation: Work Smarter Not HarderStanford Synchrotron Radiation Laboratory—30th Annual Users’ Meeting
October 8, 2003
Paul Adams, Computational Crystallography Initiative
Thomas Earnest, Berkeley Center for Structural Biology
Robohutch: Sector 5 Beamlines
Magnetic pins
112 Samples
Tools
Auto-centering
Shipping dewar
Robohutch
Magnetic pins
112 Samples
Tools
Auto-centering
Shipping dewar
Robohutch
Initial Data Entry
The Screening Interface
How many images should I collect?
Symmetry results based on… Two images 90° apartOne Image
0.5 mm
Orthorhombic(correct)
WrongIndexing
Monoclinic(not quite correct)
NoIndexing
ConventionalAutoindexing
Beam CenterPredetermination
True Beam Center
Fix Misindexing With LABELIT
• Common experience: the predicted pattern looks almost right, but something is “funny”
• Systematic absence of h + k odd
• Easily detected and corrected, once the problem is recognized
Data Processing Sequence
Collect 2 oscillationframes 90° apart
Characterize thediffraction pattern
DISTL(Ashley Deacon, SSRL)5 seconds
Integrate
MOSFLM20 seconds
Final ScoreSuccess
Resolution cutoffMosaic spreadRMS residualGood strategy
Few overlapsNo ice rings
Well-shaped spotsMinimal diffuse scatterShort exposure time
AutoindexDetermine Bravais lattice
LABELIT15 seconds
• Heuristic score within each group: score = 1 – (.7*e– 4/resolution) – (1.5*rmsResidual) – (.02*mosaicity)• Representative results: protein Syrrx-004
Bravis Lattice:
AutomaticCalculation
GroundTruth
UnitCell
Resol.Limit(Å)
RMSResid.(mm)
MosaicSpread
(º) ScoreoP P222 a=36.5 b=64.7 c=84.2 α=90 β=90 γ=90 1.5 0.028 0.5 0.90oP P222 a=36.5 b=64.8 c=83.8 α=90 β=90 γ=90 1.7 0.042 0.8 0.85oP P222 a=36.5 b=64.7 c=83.8 α=90 β=90 γ=90 1.8 0.05 0.7 0.84oP P222 a=37.0 b=65.3 c=84.0 α=90 β=90 γ=90 1.8 0.096 0.2 0.78oP P222 a=36.5 b=65.1 c=83.4 α=90 β=90 γ=90 1.6 0.108 1.3 0.75
Software Goals
Data Repository
ScreeningCrystal
SelectionData
CollectionData
ReductionAnalysis
• Provide automation by linking separate modules
GenomicsProject
IndividualLab
• Anticipate scenarios where modules work together
Single-WavelengthAnomalousDispersion
ScreenAll
CrystalsScore Strategy
InverseBeam
Collection
Cumu-lative
EachImage
FluorescenceScan
EliminateSample
Heavy-AtomSearch
AnomalousSignal
Heavy-AtomRefinement
Acknowledgements
Computational Crystallography Initiative (LBNL)Paul Adams
Ralf Grosse-Kunstleve
Nigel Moriarty
Berkeley Center for Structural Biology (LBNL)Thomas Earnest
Robert Nordmeyer
Carl Cork
Earl Cornell
John Taylor
Stanford Synchrotron Radiation LaboratoryAshley Deacon
Zepu Zhang
Syrrx, Inc.Gyorgy Snell
MRC Laboratory of Molecular BiologyAndrew Leslie
Harry Powell
Daresbury LaboratoryMartyn Winn
