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Crystal structure of Y-family DNA polymerase Dpo4 extending from a MeFapy-dG:dC pair
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 50 MM TRIS HCL, PH 7.4, 15% PEG3350, 100MM CALCIUM DIACETATE, 2.5% GLYCEROL , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.383 α = 90 b = 103.972 β = 90 c = 52.563 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2010-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0781 APS 21-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.9 30 99.8 0.143 0.143 18.715 7.1 11809 -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) Redundancy Number Unique Reflections (All) 1 2.9 2.95 100 0.617 0.617 1.81 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.9 69.88 11228 581 98.62 0.17482 0.17162 0.1757 0.23561 0.2364 RANDOM 69.836
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.135 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 16.089 r_long_range_B_refined 13.504 r_long_range_B_other 13.497 r_scangle_other 9.851 r_mcangle_other 6.899 r_mcangle_it 6.421 r_scbond_other 6.4 r_scbond_it 5.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.135 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 16.089 r_long_range_B_refined 13.504 r_long_range_B_other 13.497 r_scangle_other 9.851 r_mcangle_other 6.899 r_mcangle_it 6.421 r_scbond_other 6.4 r_scbond_it 5.901 r_dihedral_angle_1_deg 5.786 r_mcbond_it 4.327 r_mcbond_other 4.317 r_angle_refined_deg 1.451 r_angle_other_deg 1.06 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2744 Nucleic Acid Atoms 630 Solvent Atoms 58 Heterogen Atoms 33
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling