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DNA synthesis across an abasic lesion by human DNA polymerase-iota
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FLL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Crystals grew over a period of one day, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.15 α = 90 b = 98.15 β = 90 c = 203.315 γ = 120
Symmetry Space Group P 65 2 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 ADSC QUANTUM 210 Si(111) double-crystal monochromator 2005-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 97 0.058 37.6 10.1 30070 29220
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 2.2 2.28 100 0.428 37.6 10.3
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 2FLL 2.2 39.22 26873 2347 96.96 0.21399 0.21078 0.2168 0.25146 0.2579 RANDOM 26.674
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] 0.16 0.08 0.16 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.971 r_dihedral_angle_4_deg 26.714 r_dihedral_angle_3_deg 20.271 r_dihedral_angle_1_deg 6.992 r_scangle_it 4.724 r_scbond_it 3.254 r_angle_refined_deg 2.266 r_mcangle_it 1.939 r_mcbond_it 1.072 r_symmetry_hbond_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.971 r_dihedral_angle_4_deg 26.714 r_dihedral_angle_3_deg 20.271 r_dihedral_angle_1_deg 6.992 r_scangle_it 4.724 r_scbond_it 3.254 r_angle_refined_deg 2.266 r_mcangle_it 1.939 r_mcbond_it 1.072 r_symmetry_hbond_refined 0.313 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.228 r_chiral_restr 0.162 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2876 Nucleic Acid Atoms 311 Solvent Atoms 171 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement AMoRE phasing CNS refinement JDirector data collection HKL-2000 data reduction HKL-2000 data scaling