2W7P

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W7OPDB ENTRY 2W7O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1770 MM NACL,1.35 MM KCL, 2.1 MM NA2HPO4, 0.75 MM KH2PO4, PH 7.4, 5 MM GLYCEROL, 0.5 MM EDTA, 0.5 MM DTT, 2.5 MM 2-MERCHAPTOETHANOL, 0.05% NONIDET P-40, 2.5 MM CACL2, 2.5 MM DATP, 11% PEG5000MME, 0.1 M AMMONIUM ACETATE,10 MM MES PH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.475.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.829α = 90
b = 220.847β = 90
c = 119.208γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2007-10-20MSINGLE 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
13.7144.6596.90.1510.45.42304162.5
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)
13.73.9386.40.622.95.5

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 2W7O3.7144.6523026111396.90.2360.2360.273RANDOM95.5
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]
25.2-47.3522.15
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_scangle_it2.54
c_mcangle_it2.16
c_angle_deg1.5
c_scbond_it1.45
c_mcbond_it1.19
c_improper_angle_d0.96
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_scangle_it2.54
c_mcangle_it2.16
c_angle_deg1.5
c_scbond_it1.45
c_mcbond_it1.19
c_improper_angle_d0.96
c_bond_d0.009
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 Atoms6913
Nucleic Acid Atoms1136
Solvent Atoms12
Heterogen Atoms64

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing