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- PDB-4ms5: Lambda-[Ru(TAP)2(dppz-11,12-(F)2)]2+ bound to CCGGATCCGG -

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Basic information

Entry
Database: PDB / ID: 4ms5
TitleLambda-[Ru(TAP)2(dppz-11,12-(F)2)]2+ bound to CCGGATCCGG
ComponentsDNA
KeywordsDNA / Intercalation / semi-intercalation / ruthenium
Function / homology: / Chem-RKF / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsHall, J.P. / Cardin, C.J.
CitationJournal: Thesis, University of Reading / Year: 2014
Title: The effects of disubstitution on the binding of ruthenium complexes to DNA
Authors: Hall, J.P.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9673
Polymers3,0461
Non-polymers9212
Water27015
1
A: DNA
hetero molecules

A: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9346
Polymers6,0922
Non-polymers1,8424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2020 Å2
ΔGint-31 kcal/mol
Surface area4360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.610, 47.610, 34.600
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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesised by ATDBio
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-RKF / (11,12-difluorodipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)


Mass: 783.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H20F2N12Ru
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 1ul 1mM (CCGGATCCGG)2, 1ul 2mM Ru(TAP)2(dppz-11,12-(F)2]Cl2, 6ul of 40mM Na-cacodylate, 12mM spermine, 20mM BaCl2, 80mM KCl, 10% 2-methyl-2,4-pentanediol. Equilibriated against 1ml 35% 2- ...Details: 1ul 1mM (CCGGATCCGG)2, 1ul 2mM Ru(TAP)2(dppz-11,12-(F)2]Cl2, 6ul of 40mM Na-cacodylate, 12mM spermine, 20mM BaCl2, 80mM KCl, 10% 2-methyl-2,4-pentanediol. Equilibriated against 1ml 35% 2-methyl-2,4-pentanediol, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2012
RadiationMonochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 2.23→34.6 Å / Num. all: 2136 / Num. obs: 2136 / % possible obs: 99 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.23→2.29 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QRN

3qrn


Resolution: 2.23→28.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.526 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24525 95 4.5 %RANDOM
Rwork0.21882 ---
all0.22011 2016 --
obs0.22011 2016 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.23→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 54 15 271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013292
X-RAY DIFFRACTIONr_bond_other_d0.0920.02132
X-RAY DIFFRACTIONr_angle_refined_deg2.4331.61460
X-RAY DIFFRACTIONr_angle_other_deg1.8633304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02176
X-RAY DIFFRACTIONr_gen_planes_other0.0090.0274
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2793.726292
X-RAY DIFFRACTIONr_scbond_other3.2733.723293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7285.557461
X-RAY DIFFRACTIONr_long_range_B_refined6.0339.9693
X-RAY DIFFRACTIONr_long_range_B_other6.03139.902692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.231→2.289 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 10 -
Rwork0.356 146 -
obs--99.36 %

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