5YTF

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


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
2.1843.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.69α = 90
b = 107.69β = 90
c = 90.319γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2016-12-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.9793SSRFBL17U1

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
11.9893.26100115.340333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.03

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 REPLACEMENTTHROUGHOUT4DFK1.9893.2640333212799.960.183360.180730.23256RANDOM34.465
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]
0.580.290.58-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.191
r_dihedral_angle_4_deg18.856
r_dihedral_angle_3_deg15.845
r_dihedral_angle_1_deg10.238
r_long_range_B_refined3.318
r_long_range_B_other3.318
r_scangle_other1.791
r_angle_refined_deg1.768
r_mcangle_it1.307
r_mcangle_other1.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.191
r_dihedral_angle_4_deg18.856
r_dihedral_angle_3_deg15.845
r_dihedral_angle_1_deg10.238
r_long_range_B_refined3.318
r_long_range_B_other3.318
r_scangle_other1.791
r_angle_refined_deg1.768
r_mcangle_it1.307
r_mcangle_other1.307
r_angle_other_deg1.219
r_scbond_it1.108
r_scbond_other1.108
r_mcbond_it0.83
r_mcbond_other0.827
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4278
Nucleic Acid Atoms573
Solvent Atoms358
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing