2W9B

Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.4DPO4:DNA COMPLEX (1:1.2 MOLAR RATIO, 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 1 MM DGTP.
Crystal Properties
Matthews coefficientSolvent content
2.4253.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.794α = 90
b = 101.776β = 91.95
c = 97.268γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2008-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

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
12.2828.7596.40.110.33.94562541
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)
12.282.4289.70.263.86.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ASD2.2828.7544372223196.40.2390.2390.251RANDOM36.3
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]
1.382.31-5.524.14
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.5
c_scangle_it3.64
c_angle_deg3.2
c_scbond_it2.75
c_improper_angle_d2.39
c_mcangle_it2.27
c_mcbond_it1.4
c_bond_d0.034
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.5
c_scangle_it3.64
c_angle_deg3.2
c_scbond_it2.75
c_improper_angle_d2.39
c_mcangle_it2.27
c_mcbond_it1.4
c_bond_d0.034
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5500
Nucleic Acid Atoms1220
Solvent Atoms203
Heterogen Atoms4

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing