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- PDB-1d18: SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUC... -
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Basic information
Entry | Database: PDB / ID: 1d18 | ||||||||||||||||||
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Title | SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / DOUBLE HELIX | Function / homology | DNA | ![]() Method | SOLUTION NMR / ENERGY MINIMIZATION, MOLECULAR DYNAMICS | ![]() Baleja, J.D. / Sykes, B.D. | ![]() ![]() Title: Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement. Authors: Baleja, J.D. / Germann, M.W. / van de Sande, J.H. / Sykes, B.D. #1: ![]() Title: Distance Measurement and Structure Refinement with Noe Data Authors: Baleja, J.D. / Moult, J. / Sykes, B.D. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 19 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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Processing
NMR software | Name: GROMOS / Developer: DE VLIEG ET AL / Classification: refinement |
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Refinement | Method: ENERGY MINIMIZATION, MOLECULAR DYNAMICS / Software ordinal: 1 Details: THE STRUCTURE WAS REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.23 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES ...Details: THE STRUCTURE WAS REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.23 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION TIME ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO THE INVERSE OF THE TEMPERATURE FACTORS ASSOCIATED WITH X-RAY CRYSTALLOGRAPHY. THESE VALUES ARE INCLUDED IN THE COLUMN NORMALLY USED FOR TEMPERATURE FACTORS. VALUES OF 0.0 APPEAR FOR NON-HYDROGEN ATOMS, WHICH WERE NOT USED IN THE NMR CALCULATIONS. FURTHER DETAILS ARE GIVEN IN REFERENCE 1. |
NMR ensemble | Conformers submitted total number: 1 |