5YTG

Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base I-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
2.2445.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.063α = 90
b = 109.063β = 90
c = 90.935γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2015-11-29MSINGLE 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
12.0794.4599.722.956.136400
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.11

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 REPLACEMENTTHROUGHOUT4DFK2.0794.4536400186099.650.200770.198060.25203RANDOM48.442
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]
0.610.310.61-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.567
r_dihedral_angle_4_deg17.883
r_dihedral_angle_3_deg15.184
r_dihedral_angle_1_deg9.345
r_long_range_B_refined3.368
r_long_range_B_other3.368
r_scangle_other1.519
r_angle_refined_deg1.498
r_mcangle_it1.26
r_mcangle_other1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.567
r_dihedral_angle_4_deg17.883
r_dihedral_angle_3_deg15.184
r_dihedral_angle_1_deg9.345
r_long_range_B_refined3.368
r_long_range_B_other3.368
r_scangle_other1.519
r_angle_refined_deg1.498
r_mcangle_it1.26
r_mcangle_other1.26
r_angle_other_deg1.127
r_scbond_it0.891
r_scbond_other0.891
r_mcbond_it0.769
r_mcbond_other0.768
r_chiral_restr0.089
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms577
Solvent Atoms271
Heterogen Atoms40

Software

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