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- PDB-3qba: Reintroducing Electrostatics into Macromolecular Crystallographic... -

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Basic information

Entry
Database: PDB / ID: 3qba
TitleReintroducing Electrostatics into Macromolecular Crystallographic Refinement: Z-DNA (X-ray)
ComponentsZ-DNA
KeywordsDNA / Z-DNA
Function / homologyDEUTERATED WATER / DNA
Function and homology information
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsFenn, T.D. / Schnieders, M.J. / Mustyakimov, M. / Wu, C. / Langan, P. / Pande, V.S. / Brunger, A.T.
CitationJournal: Structure / Year: 2011
Title: Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
Authors: Fenn, T.D. / Schnieders, M.J. / Mustyakimov, M. / Wu, C. / Langan, P. / Pande, V.S. / Brunger, A.T.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Data collection
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Z-DNA
B: Z-DNA


Theoretical massNumber of molelcules
Total (without water)3,4602
Polymers3,4602
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-9 kcal/mol
Surface area4310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.900, 30.590, 44.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain Z-DNA


Mass: 1730.225 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: solid state synthesis using a phosphoramidite approach
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 0.01M Magnesium Acetate 0.05M MES pH 5.6 2.5M Ammonium Sulfate, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E DW11.54
NUCLEAR REACTOR20.6-0.7
Detector
TypeIDDetectorDate
RIGAKU SATURN 921CCDJan 1, 2006
2AREA DETECTORJan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.61
30.71
ReflectionResolution: 1.53→100 Å / Num. all: 3696 / Num. obs: 3696 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
CrystalCleardata collection
PHASERphasing
nCNS-TINKERrefinement
d*TREKdata reduction
SCALAdata scaling
Refinement

R Free selection details: random, throughout / σ(F): 0 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: AMOEBA

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obsDiffraction-ID
1.53-100X-RAY DIFFRACTION0.23590.1937178369636961
1.4-100NEUTRON DIFFRACTION0.31470.3007240468046802
Refinement stepCycle: LAST / Resolution: 1.53→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 41 281

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