3EZ5

Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8290Ammonium Sulfate, MES, MPD, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5952.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.551α = 90
b = 108.572β = 90
c = 149.756γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2004-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.282420APS22-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
11.95099.90.05812.283.78119138-339.668
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)
1.921000.3983.43.7121167

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 DIFFRACTIONTHROUGHOUTPDB ENTRY 2HVI1.946.83-3119174119138501099.970.2120.2110.244RANDOM in 1.98-1.90 shell, inherited from 2HVI data set in 50-1.98 shell37.225
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.001
r_dihedral_angle_4_deg18.627
r_dihedral_angle_3_deg14.694
r_dihedral_angle_1_deg5.246
r_scangle_it3.438
r_scbond_it2.126
r_mcangle_it1.388
r_angle_refined_deg1.382
r_mcbond_it0.729
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.001
r_dihedral_angle_4_deg18.627
r_dihedral_angle_3_deg14.694
r_dihedral_angle_1_deg5.246
r_scangle_it3.438
r_scbond_it2.126
r_mcangle_it1.388
r_angle_refined_deg1.382
r_mcbond_it0.729
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9312
Nucleic Acid Atoms846
Solvent Atoms540
Heterogen Atoms124

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction