7N2M

Crystal structure of DNA polymerase alpha catalytic core in complex with dCTP and template/primer having T-C mismatch at the post-insertion site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QCL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52950.8 mM zinc sulfate, 8.8% v/v PEG MME 550, and 50 mM MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.5272.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.285α = 90
b = 140.285β = 90
c = 181.066γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9795APS24-ID-C

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
12.95098.70.07929.35.54558233.4
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)
12.92.9597.70.4373.23.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4qcl2.944.5145573228898.70.1950.228RANDOM51.1
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]
-0.9912.48-0.991.99
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.9
c_angle_deg1.4
c_improper_angle_d0.99
c_bond_d0.008
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6948
Nucleic Acid Atoms494
Solvent Atoms110
Heterogen Atoms55

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
CNSrefinement
PDB_EXTRACTdata extraction