3LPV

X-ray crystal structure of duplex DNA containing a cisplatin 1,2-d(GpG) intrastrand cross-link


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277120 mM Magnesium Acetate, 50 mM Sodium Cacodylate pH 6.5, 28% w/v PEG-4000, 1 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3262.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.303α = 80.06
b = 35.425β = 84.09
c = 45.128γ = 81.77
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDRh coated flat mirror, toroidal focusing mirror2009-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.979SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7750960.09215.62.91763917639
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.771.8385.20.3892.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1AIO1.7744.31176241674589196.250.173420.172120.19788RANDOM39.042
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.530.091.75-0.341.310.03
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.84
r_scbond_it1.895
r_angle_refined_deg1.883
r_mcbond_it0.315
r_nbd_other0.265
r_nbtor_refined0.263
r_symmetry_hbond_refined0.216
r_symmetry_vdw_other0.166
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_refined0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it2.84
r_scbond_it1.895
r_angle_refined_deg1.883
r_mcbond_it0.315
r_nbd_other0.265
r_nbtor_refined0.263
r_symmetry_hbond_refined0.216
r_symmetry_vdw_other0.166
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_refined0.146
r_nbd_refined0.105
r_chiral_restr0.08
r_nbtor_other0.074
r_metal_ion_refined0.041
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms972
Solvent Atoms148
Heterogen Atoms10

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling