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- PDB-2h05: Br Derivitation of A-DNA Octamer GTG(Ubr)ACAC -

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Basic information

Entry
Database: PDB / ID: 2h05
TitleBr Derivitation of A-DNA Octamer GTG(Ubr)ACAC
Components5'-D(*GP*TP*GP*(BRU)P*AP*CP*AP*C)-3'
KeywordsDNA / Br-DNA / Se-DNA / Se-Br-DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, SAD / Resolution: 1.8 Å
AuthorsJiang, J. / Sheng, J. / Huang, Z.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Selenium derivatization of nucleic acids for crystallography.
Authors: Jiang, J. / Sheng, J. / Carrasco, N. / Huang, Z.
History
DepositionMay 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: 5'-D(*GP*TP*GP*(BRU)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)2,4911
Polymers2,4911
Non-polymers00
Water59433
1
A: 5'-D(*GP*TP*GP*(BRU)P*AP*CP*AP*C)-3'

A: 5'-D(*GP*TP*GP*(BRU)P*AP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,9832
Polymers4,9832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)42.048, 42.048, 24.270
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 5'-D(*GP*TP*GP*(BRU)P*AP*CP*AP*C)-3'


Mass: 2491.487 Da / Num. of mol.: 1 / Mutation: 5-BROMO-Modified T4, BRU / Source method: obtained synthetically
Details: Solid Phase Synthesis via Phosphoramidite Chemistry
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8mM MgCl2, 4mM Spermine, 40% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2Spermine11
3MPD11
4H2O11
5MgCl212
6Spermine12
7MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9199, 0.9202, 0.9400, 1.100
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2006
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91991
20.92021
30.941
41.11
ReflectionResolution: 1.8→18.81 Å / Num. all: 2248 / Num. obs: 2248 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7 / Num. unique all: 203 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD, SAD
Starting model: pdb entry 1Z7I

1z7i


Resolution: 1.8→18.81 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 532897.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: DNA-RNA
RfactorNum. reflection% reflectionSelection details
Rfree0.248 188 9.2 %RANDOM
Rwork0.213 ---
all0.22 2036 --
obs0.213 2036 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4104 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2--2.2 Å20 Å2
3----4.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 33 194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d28.3
X-RAY DIFFRACTIONc_improper_angle_d2.16
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.078 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 28 10.2 %
Rwork0.273 247 -
obs-247 75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4dna-rna_ums.parion.top

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