3F2D

DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mn and Zn


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F2BPDB entry 3F2B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.328920% PEG 2000 MME, 0.1M PHOSPHATE CITRATE, 200MM LITHIUM SULFATE, 1 mM ZnCl2, 2 mM MnCl2, pH 5.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.8757.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.997α = 90
b = 139.479β = 90
c = 184.074γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.999887ALS5.0.1

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
12.543.1599.80.08711.24.950821
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)
12.52.59990.6424.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3F2B2.5143.155075025730.2180.2160.254RANDOM46.38
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]
-2.161.011.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.525
r_dihedral_angle_3_deg20.591
r_dihedral_angle_4_deg18.887
r_dihedral_angle_1_deg5.964
r_scangle_it2.479
r_angle_refined_deg1.701
r_scbond_it1.547
r_mcangle_it0.934
r_mcbond_it0.48
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.525
r_dihedral_angle_3_deg20.591
r_dihedral_angle_4_deg18.887
r_dihedral_angle_1_deg5.964
r_scangle_it2.479
r_angle_refined_deg1.701
r_scbond_it1.547
r_mcangle_it0.934
r_mcbond_it0.48
r_chiral_restr0.101
r_bond_refined_d0.013
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 Atoms7796
Nucleic Acid Atoms631
Solvent Atoms101
Heterogen Atoms46

Software

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