8XK7 | pdb_00008xk7

binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherstructure of apo SFM4-3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, and 28% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9458.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.61α = 90
b = 65.628β = 103.51
c = 107.378γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
125098.80.1350.1480.060.9744.36.155909
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0399.70.5860.640.2550.9156.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT224.4153014283298.770.193470.191510.20120.23110.2324RANDOM36.354
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]
1.66-1.333.74-4.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.286
r_dihedral_angle_2_deg12.959
r_long_range_B_refined5.957
r_long_range_B_other5.957
r_dihedral_angle_1_deg5.837
r_scangle_other4.326
r_mcangle_other3.294
r_mcangle_it3.293
r_scbond_it2.843
r_scbond_other2.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.286
r_dihedral_angle_2_deg12.959
r_long_range_B_refined5.957
r_long_range_B_other5.957
r_dihedral_angle_1_deg5.837
r_scangle_other4.326
r_mcangle_other3.294
r_mcangle_it3.293
r_scbond_it2.843
r_scbond_other2.842
r_mcbond_it2.282
r_mcbond_other2.282
r_angle_refined_deg1.363
r_angle_other_deg0.386
r_chiral_restr0.081
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms4315
Nucleic Acid Atoms619
Solvent Atoms346
Heterogen Atoms32

Software

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