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- PDB-341d: STRUCTURAL PARAMETERS FROM SINGLE-CRYSTAL STRUCTURES FOR ACCURATE... -

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Basic information

Entry
Database: PDB / ID: 341d
TitleSTRUCTURAL PARAMETERS FROM SINGLE-CRYSTAL STRUCTURES FOR ACCURATE MODELS OF A-DNA
ComponentsDNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionJun 26, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 21, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _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*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4571
Polymers2,4571
Non-polymers00
Water41423
1
A: DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)4,9132
Polymers4,9132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)42.810, 42.810, 24.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2456.647 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Description: CRYSTALLIZED IN THE PRESENCE OF MAGNESIUM CHLORIDE
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MGCL212

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Data collection

DiffractionMean temperature: 298 K
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.71→30.3 Å / Num. obs: 2642 / % possible obs: 71.91 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.085

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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: 1.75→7.7 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.185 -
obs0.185 1976
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→7.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 2 23 186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.41
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: GMGMMG.PAR / Topol file: TOP.DNA

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