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Ternary Crystal Structures of a Y-family DNA polymerase DPO4 from Sulfobus Solfataricus in Comples with DNA and L-DCDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 16% PEG 3350, 0.1 M HEPES (PH 7.0), 100MM CALCIUM ACETATE, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.44 α = 90 b = 101.93 β = 90 c = 105.4 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX225HE 2012-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 49.22 99.3 41845
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.892 2.8 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4FO3 2.4 46.46 39665 2110 99.16 0.22983 0.22728 0.2325 0.27705 0.2818 RANDOM 70.557
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] -0.47 0.3 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_3_deg 18.791 r_dihedral_angle_4_deg 14.17 r_dihedral_angle_1_deg 5.835 r_mcangle_it 3.587 r_scbond_it 2.173 r_mcbond_it 2.109 r_mcbond_other 2.109 r_angle_other_deg 1.239 r_angle_refined_deg 1.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_3_deg 18.791 r_dihedral_angle_4_deg 14.17 r_dihedral_angle_1_deg 5.835 r_mcangle_it 3.587 r_scbond_it 2.173 r_mcbond_it 2.109 r_mcbond_other 2.109 r_angle_other_deg 1.239 r_angle_refined_deg 1.237 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5504 Nucleic Acid Atoms 1108 Solvent Atoms 175 Heterogen Atoms 101
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling