2XCP

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dCTP - MAGNESIUM FORM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C2EPDB ENTRY 2C2E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5RESERVOIR:12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, AND 20 MM TRIS (PH 7.5) DROP: 10MM TRIS-CL PH 7.5, 30 MM NACL, 0.5MM DCTP, 2.5MM MGCL2, 6-10% POLYETHYLENE GLYCOL 3350, 0.1M AMMONIUM ACETATE, 0.05M MAGNESIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
3.6759.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.757α = 90
b = 100.429β = 96.08
c = 105.873γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHROSENBAUM-ROCK MONOCHROMATOR HIGH -RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR2007-06-03MSINGLE 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
12.649.598.10.0714.85.237629147
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)
12.62.7690.10.493.73.8

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 2C2E2.649.5537629187498.10.2230.2230.268RANDOM48.3
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]
4.253.08-0.02-4.23
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.1
c_scangle_it3.09
c_mcangle_it2.29
c_scbond_it1.98
c_mcbond_it1.33
c_angle_deg1.3
c_improper_angle_d1
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.1
c_scangle_it3.09
c_mcangle_it2.29
c_scbond_it1.98
c_mcbond_it1.33
c_angle_deg1.3
c_improper_angle_d1
c_bond_d0.007
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 Atoms5498
Nucleic Acid Atoms1223
Solvent Atoms305
Heterogen Atoms62

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing