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- PDB-242d: MAD PHASING STRATEGIES EXPLORED WITH A BROMINATED OLIGONUCLEOTIDE... -

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Basic information

Entry
Database: PDB / ID: 242d
TitleMAD PHASING STRATEGIES EXPLORED WITH A BROMINATED OLIGONUCLEOTIDE CRYSTAL AT 1.65 A RESOLUTION.
ComponentsDNA (5'-D(*CP*GP*CP*GP*(CBR)P*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsPeterson, M.R. / Harrop, S.J. / McSweeney, S.M. / Leonard, G.A. / Thompson, A.W. / Hunter, W.N. / Helliwell, J.R.
Citation
Journal: J.Synchrotron Radiat. / Year: 1996
Title: MAD Phasing Strategies Explored with a Brominated Oligonucleotide Crystal at 1.65A Resolution.
Authors: Peterson, M.R. / Harrop, S.J. / McSweeney, S.M. / Leonard, G.A. / Thompson, A.W. / Hunter, W.N. / Helliwell, J.R.
#1: Journal: Nature / Year: 1979
Title: Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution
Authors: Wang, A.H.-J. / Quigley, G.J. / Kolpak, F.J. / Crawford, J.L. / Van Boom, J.H. / Van Der Marel, G. / Rich, A.
History
DepositionJun 20, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 19, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*(CBR)P*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*(CBR)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,7782
Polymers3,7782
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.970, 30.980, 44.850
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 DNA (5'-D(*CP*GP*CP*GP*(CBR)P*G)-3')


Mass: 1889.101 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.65 Å3/Da / Density % sol: 25.55 %
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
MLPHAREphasing
NUCLSQrefinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.65→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.17 3151
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 2 61 303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d1.4130.01
X-RAY DIFFRACTIONn_angle_d2.4040.15
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d1.5420.01
X-RAY DIFFRACTIONn_phos_bond_angle_d3.0450.15
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.015
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr

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