3PX0

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HVIPDB entry 2HVI with insertion site base pair, metal ions, waters, and protein residues 680-717 deleted

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8290Ammonium Sulfate, MPD, MgSO4, MnSO4, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5952.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.91α = 90
b = 108.96β = 90
c = 150.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCD2010-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-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
11.7310098.30.05817.995.8160634157944-3
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)
11.731.8399.60.5832.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISPDB entry 2HVI with insertion site base pair, metal ions, waters, and protein residues 680-717 deleted1.7334.2422.35160634149632668793.170.19650.19520.2236Inherited free reflections from 2HVI plus randomly generated reflections beyond 1.98 resolution
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]
0.45660.5793-1.0359
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.108
f_angle_d1.193
f_chiral_restr0.068
f_bond_d0.009
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9119
Nucleic Acid Atoms848
Solvent Atoms1368
Heterogen Atoms106

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling