3TI0

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddGTP-dC in Closed Conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HVIPDB ENTRY 2HVI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.829045-50% saturated ammonium sulfate, 2.5% MPD, 10 mM magnesium sulfate, 100 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5752.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.5α = 90
b = 108.92β = 90
c = 149.57γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.97121APS22-BM

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
11.6210098.30.07312.2190278-3
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)
11.621.7199.60.4933.46

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISPDB ENTRY 2HVI1.6242.962.35180731820493.360.18790.18660.215
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]
1.5157-2.17470.6589
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.202
f_angle_d1.221
f_chiral_restr0.065
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9293
Nucleic Acid Atoms844
Solvent Atoms1687
Heterogen Atoms72

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing