3H8R | pdb_00003h8r

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5277PEG 5000, NaCl, MgCl2, Cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1861.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.08α = 90
b = 78.08β = 90
c = 228.71γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.771599.920.3383711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8199.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.77153840138371199399.90.2120.210.210.2360.23RANDOM29.17
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]
0.550.280.55-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.448
r_dihedral_angle_4_deg14.219
r_dihedral_angle_3_deg13.761
r_dihedral_angle_1_deg6.288
r_scangle_it2.719
r_scbond_it1.724
r_angle_refined_deg1.534
r_mcangle_it1.233
r_mcbond_it0.678
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.448
r_dihedral_angle_4_deg14.219
r_dihedral_angle_3_deg13.761
r_dihedral_angle_1_deg6.288
r_scangle_it2.719
r_scbond_it1.724
r_angle_refined_deg1.534
r_mcangle_it1.233
r_mcbond_it0.678
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1640
Nucleic Acid Atoms528
Solvent Atoms218
Heterogen Atoms14

Software

Software
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling