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binary complex of catalytic core of human DNA polymerase iota with DNA (template A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ALZ PDB CODE 2ALZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.67 54.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.114 α = 90 b = 98.114 β = 90 c = 202.823 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-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 2.5 50 99.1 0.058 33.5 10.32 20742 19908
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB CODE 2ALZ 2.5 39.22 20742 17861 1973 95.69 0.2309 0.22554 0.27864 0.2968 RANDOM 45.346
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] 0.61 0.3 0.61 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.587 r_scangle_it 5.576 r_scbond_it 4.011 r_mcangle_it 3.336 r_angle_refined_deg 2.961 r_mcbond_it 1.966 r_symmetry_hbond_refined 0.392 r_symmetry_vdw_refined 0.345 r_nbd_refined 0.293 r_xyhbond_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.587 r_scangle_it 5.576 r_scbond_it 4.011 r_mcangle_it 3.336 r_angle_refined_deg 2.961 r_mcbond_it 1.966 r_symmetry_hbond_refined 0.392 r_symmetry_vdw_refined 0.345 r_nbd_refined 0.293 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.185 r_bond_refined_d 0.035 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 2797 Nucleic Acid Atoms 321 Solvent Atoms 101 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing