5YTH

Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DFK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7293.150.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2645.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.273α = 90
b = 109.273β = 90
c = 91.119γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9793SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.5394.6399.918.766.820264
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.532.57

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 REPLACEMENTTHROUGHOUT4DFK2.5394.6320264105999.770.207240.203690.27457RANDOM59.834
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]
0.660.330.66-2.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.141
r_dihedral_angle_4_deg17.884
r_dihedral_angle_3_deg17.519
r_dihedral_angle_1_deg7.883
r_long_range_B_refined1.737
r_long_range_B_other1.736
r_angle_refined_deg1.309
r_angle_other_deg0.981
r_mcangle_it0.801
r_mcangle_other0.801
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.141
r_dihedral_angle_4_deg17.884
r_dihedral_angle_3_deg17.519
r_dihedral_angle_1_deg7.883
r_long_range_B_refined1.737
r_long_range_B_other1.736
r_angle_refined_deg1.309
r_angle_other_deg0.981
r_mcangle_it0.801
r_mcangle_other0.801
r_scangle_other0.799
r_mcbond_it0.462
r_mcbond_other0.462
r_scbond_it0.453
r_scbond_other0.453
r_chiral_restr0.068
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4266
Nucleic Acid Atoms573
Solvent Atoms75
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing