4RUA

Crystal structure of Y-family DNA polymerase Dpo4 bypassing a MeFapy-dG adduct


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429850 MM TRIS HCL,PH 7.4, 15% PEG3350, 100MM CALCIUM DIACETATE, 2.5% GLYCEROL , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.754.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.451α = 90
b = 102.716β = 90
c = 53.432γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07810APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
13.0685098.40.1120.11216.3786.210134-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.1584.70.680.681.0723.1

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 REPLACEMENTTHROUGHOUTPDB code 2BQU3.0750961252198.020.168430.16330.25827RANDOM88.239
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]
1.29-0.92-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_3_deg18.14
r_long_range_B_refined15.826
r_long_range_B_other15.826
r_dihedral_angle_4_deg12.19
r_scangle_other11.388
r_mcangle_it8.542
r_mcangle_other8.315
r_scbond_it7.66
r_scbond_other7.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_3_deg18.14
r_long_range_B_refined15.826
r_long_range_B_other15.826
r_dihedral_angle_4_deg12.19
r_scangle_other11.388
r_mcangle_it8.542
r_mcangle_other8.315
r_scbond_it7.66
r_scbond_other7.27
r_dihedral_angle_1_deg6.949
r_mcbond_other5.713
r_mcbond_it5.712
r_angle_refined_deg1.527
r_angle_other_deg1.267
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms2744
Nucleic Acid Atoms611
Solvent Atoms36
Heterogen Atoms33

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling