3F2C

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


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, 2 mM MnCl2, PH 5.3, VAPOR DIFFUSION , pH 5.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9257.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.889α = 90
b = 141.185β = 90
c = 184.74γ = 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
12.543.699.10.09105.951829
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)
12.52.5991.70.5893.9

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 3F2B2.543.65179126410.2130.210.255RANDOM39.53
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]
-1.822.62-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.351
r_dihedral_angle_4_deg20.862
r_dihedral_angle_3_deg20.096
r_dihedral_angle_1_deg5.865
r_scangle_it2.079
r_angle_refined_deg1.452
r_scbond_it1.259
r_mcangle_it0.772
r_mcbond_it0.391
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.351
r_dihedral_angle_4_deg20.862
r_dihedral_angle_3_deg20.096
r_dihedral_angle_1_deg5.865
r_scangle_it2.079
r_angle_refined_deg1.452
r_scbond_it1.259
r_mcangle_it0.772
r_mcbond_it0.391
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms155
Heterogen Atoms40

Software

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