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- PDB-346d: STRUCTURAL PARAMETERS FROM SINGLE-CRYSTAL STRUCTURES FOR ACCURATE... -

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Basic information

Entry
Database: PDB / ID: 346d
TitleSTRUCTURAL PARAMETERS FROM SINGLE-CRYSTAL STRUCTURES FOR ACCURATE MODELS OF A-DNA
ComponentsDNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*(5CM)P*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMooers, B.H.M. / Eichman, B.F. / Ho, P.S.
CitationJournal: To be Published
Title: Structural Parameters from Single-Crystal Structures for Accurate Models of A-DNA
Authors: Mooers, B.H.M. / Eichman, B.F. / Ho, P.S.
History
DepositionAug 26, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 29, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*(5CM)P*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4711
Polymers2,4711
Non-polymers00
Water32418
1
A: DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*(5CM)P*GP*C)-3')

A: DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*(5CM)P*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,9412
Polymers4,9412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)43.480, 43.480, 25.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-15-

HOH

21A-16-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*(5CM)P*GP*C)-3')


Mass: 2470.674 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutionsName: WATER

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Data collection

DiffractionMean temperature: 298 K
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jun 25, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→12.1 Å / Num. obs: 2153 / % possible obs: 76.97 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.048

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Processing

Software
NameVersionClassification
XTALVIEWrefinement
X-PLORmodel building
X-PLOR3.1refinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.204 -
obs0.204 1371
Displacement parametersBiso mean: 21.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 3 18 182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PAR.DNA / Topol file: TOP.DNA

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