5YTD

large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the natural base pair 5fC:dGTP


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
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.909α = 90
b = 108.909β = 90
c = 90.539γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2014-09-03MSINGLE 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
1294.3299.823.687.240252
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.03

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 REPLACEMENTTHROUGHOUT4DFK294.3240252213799.80.198220.196080.2387RANDOM52.76
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]
0.980.490.98-3.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.003
r_dihedral_angle_4_deg17.598
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg8.951
r_long_range_B_refined4.572
r_long_range_B_other4.438
r_scangle_other1.79
r_mcangle_it1.574
r_mcangle_other1.574
r_angle_refined_deg1.348
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.003
r_dihedral_angle_4_deg17.598
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg8.951
r_long_range_B_refined4.572
r_long_range_B_other4.438
r_scangle_other1.79
r_mcangle_it1.574
r_mcangle_other1.574
r_angle_refined_deg1.348
r_angle_other_deg1.099
r_scbond_other1.064
r_scbond_it1.063
r_mcbond_it0.982
r_mcbond_other0.981
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.003
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 Atoms4286
Nucleic Acid Atoms569
Solvent Atoms239
Heterogen Atoms33

Software

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