2C2D

Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C28PDB ENTRY 2C28

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.55% PEG 3350, 10 MM TRIS-HCL PH 7.5, 50 MM CA(CH3CO2)2, 30MM NACL, 1.25% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.7154.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.507α = 90
b = 102.017β = 90
c = 53.093γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCD2005-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
12.5643.99970.0916.489.7817022180.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.562.7281.7

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 2C282.5743.9917021828970.240.240.28RANDOM78.6
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]
6.42-3.25-3.17
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_mcangle_it2.94
c_scangle_it2.85
c_angle_deg1.9
c_scbond_it1.72
c_mcbond_it1.64
c_improper_angle_d1.22
c_bond_d0.011
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_mcangle_it2.94
c_scangle_it2.85
c_angle_deg1.9
c_scbond_it1.72
c_mcbond_it1.64
c_improper_angle_d1.22
c_bond_d0.011
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 Atoms2744
Nucleic Acid Atoms569
Solvent Atoms96
Heterogen Atoms65

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing