4DSK

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, PPi and Calcium


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.50.2 M calcium acetate, 0.1 M sodium cacodylate (pH 6.5), 18% v/v PEG8000, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8556.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.692α = 90
b = 93.339β = 90
c = 106.363γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2011-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12B1.0000NSLSX12B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.1870.1696.90.08519.85.64571244295
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.182.2678.50.3742.22.34497

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3HT32.1870.164571239669443396.480.19090.19090.185090.24275RANDOM32.076
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]
1.87-1.11-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.03
r_dihedral_angle_4_deg18.785
r_dihedral_angle_3_deg17.744
r_dihedral_angle_1_deg5.919
r_scangle_it4.807
r_scbond_it2.988
r_mcangle_it1.767
r_angle_refined_deg1.758
r_mcbond_it0.896
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.03
r_dihedral_angle_4_deg18.785
r_dihedral_angle_3_deg17.744
r_dihedral_angle_1_deg5.919
r_scangle_it4.807
r_scbond_it2.988
r_mcangle_it1.767
r_angle_refined_deg1.758
r_mcbond_it0.896
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4617
Nucleic Acid Atoms497
Solvent Atoms300
Heterogen Atoms13

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling