4RUC

Crystal structure of Y-family DNA polymerase Dpo4 extending from a MeFapy-dG:dC pair


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
2.6453.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.383α = 90
b = 103.972β = 90
c = 52.563γ = 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-D1.0781APS21-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
12.93099.80.1430.14318.7157.111809-3
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)
12.92.951000.6170.6171.817.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.969.881122858198.620.174820.171620.23561RANDOM69.836
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]
2.75-0.95-1.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.135
r_dihedral_angle_4_deg17.156
r_dihedral_angle_3_deg16.089
r_long_range_B_refined13.504
r_long_range_B_other13.497
r_scangle_other9.851
r_mcangle_other6.899
r_mcangle_it6.421
r_scbond_other6.4
r_scbond_it5.901
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.135
r_dihedral_angle_4_deg17.156
r_dihedral_angle_3_deg16.089
r_long_range_B_refined13.504
r_long_range_B_other13.497
r_scangle_other9.851
r_mcangle_other6.899
r_mcangle_it6.421
r_scbond_other6.4
r_scbond_it5.901
r_dihedral_angle_1_deg5.786
r_mcbond_it4.327
r_mcbond_other4.317
r_angle_refined_deg1.451
r_angle_other_deg1.06
r_chiral_restr0.075
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 Atoms630
Solvent Atoms58
Heterogen Atoms33

Software

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