4X35 | pdb_00004x35

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

• PDB DOI: https://doi.org/10.2210/pdb4X35/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Operophtera brumata cypovirus 18
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-11-27 Released: 2015-06-10 
• Deposition Author(s): Roedig, P., Vartiainen, I., Duman, R., Panneerselvam, S., Stuebe, N., Lorbeer, O., Warmer, M., Sutton, G., Stuart, D.I., Weckert, E., David, C., Wagner, A., Meents, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.170 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

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

• PubMed: 26022615 
• DOI: https://doi.org/10.1038/srep10451
• Primary Citation 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.
Paul Scherrer Institut, Villigen PSI, 5232, Switzerland.
Diamond Light Source Ltd., Diamond House, Harwell Science &Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom.
1] Diamond Light Source Ltd., Diamond House, Harwell Science &Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom [2] Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.51 kDa 
• Atom Count: 2,321 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyhedrin	A	248	Operophtera brumata cypovirus 18	Mutation(s): 0
UniProt
Find proteins for Q30C70 (Operophtera brumata cypovirus 18) Explore Q30C70  Go to UniProtKB:  Q30C70

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	E [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP	F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.170 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.81	α = 90
b = 102.81	β = 90
c = 102.81	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Roedig, P., Vartiainen, I., Duman, R., Panneerselvam, S., Stuebe, N., Lorbeer, O., Warmer, M., Sutton, G., Stuart, D.I., Weckert, E., David, C., Wagner, A., Meents, A.

Revision History  

• 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