2W8L

Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in anti orientation


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, 4% GLYCEROL, 1 MM DGTP.
Crystal Properties
Matthew coefficientSolvent content
2.6152.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.919α = 90
b = 103.832β = 90
c = 52.493γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2008-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
1342.1199.60.0823.376.61175157.3
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)
133.191000.774.77.3

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 2BQR329.251058456098.50.2260.2260.282RANDOM77.4
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]
5.56-1.48-4.09
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it3.5
c_mcangle_it2.61
c_scbond_it2.25
c_improper_angle_d1.77
c_angle_deg1.6
c_mcbond_it1.5
c_bond_d0.009
c_angle_deg_prot
c_bond_d_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it3.5
c_mcangle_it2.61
c_scbond_it2.25
c_improper_angle_d1.77
c_angle_deg1.6
c_mcbond_it1.5
c_bond_d0.009
c_angle_deg_prot
c_bond_d_na
c_angle_d
c_dihedral_angle_d_prot
c_angle_d_na
c_improper_angle_d_na
c_improper_angle_d_prot
c_angle_d_prot
c_bond_d_prot
c_angle_deg_na
c_dihedral_angle_d_na
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2754
Nucleic Acid Atoms618
Solvent Atoms43
Heterogen Atoms34

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing