4X35

A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.130 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering.

Roedig, P.Vartiainen, I.Duman, R.Panneerselvam, S.Stube, N.Lorbeer, O.Warmer, M.Sutton, G.Stuart, D.I.Weckert, E.David, C.Wagner, A.Meents, A.

(2015) Sci Rep 5: 10451-10451

  • DOI: https://doi.org/10.1038/srep10451
  • Primary Citation of Related Structures:  
    4X35, 4X3B

  • PubMed Abstract: 

    At low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered too small for diffraction experiments. Conventional mounting techniques do not fulfill the requirements of these new experiments. They significantly contribute to background scattering and it is difficult to locate the crystals, making them incompatible with automated serial crystallography. We have developed a micro-fabricated sample holder from single crystalline silicon with micropores, which carries up to thousands of crystals and significantly reduces the background scattering level. For loading, the suspended microcrystals are pipetted onto the chip and excess mother liquor is subsequently soaked off through the micropores. Crystals larger than the pore size are retained and arrange themselves according to the micropore pattern. Using our chip we were able to collect 1.5 Å high resolution diffraction data from protein microcrystals with sizes of 4 micrometers and smaller.


  • Organizational Affiliation

    Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestraße 85, 22607 Hamburg.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyhedrin248Operophtera brumata cypovirus 18Mutation(s): 0 
UniProt
Find proteins for Q30C70 (Operophtera brumata cypovirus 18)
Explore Q30C70 
Go to UniProtKB:  Q30C70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ30C70
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.130 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.81α = 90
b = 102.81β = 90
c = 102.81γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 2.0: 2024-01-10
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.1: 2024-10-23
    Changes: Structure summary