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Ternary complex of human DNA polymerase iota with DNA and dTTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AZL PDB code 2AZL
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 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.329 α = 90 b = 98.329 β = 90 c = 202.186 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 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 2.6 50 99.7 0.059 34.5 7 18517 18496
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 2AZL 2.6 50 18517 16057 1376 94.19 0.22765 0.22329 0.27747 0.2648 RANDOM 42.281
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] 0.63 0.31 0.63 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.705 r_scangle_it 5.62 r_scbond_it 3.822 r_mcangle_it 3.288 r_angle_refined_deg 2.929 r_mcbond_it 1.951 r_angle_other_deg 1.522 r_symmetry_vdw_refined 0.616 r_symmetry_vdw_other 0.44 r_symmetry_hbond_refined 0.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.705 r_scangle_it 5.62 r_scbond_it 3.822 r_mcangle_it 3.288 r_angle_refined_deg 2.929 r_mcbond_it 1.951 r_angle_other_deg 1.522 r_symmetry_vdw_refined 0.616 r_symmetry_vdw_other 0.44 r_symmetry_hbond_refined 0.436 r_nbd_other 0.277 r_nbd_refined 0.264 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.177 r_nbtor_other 0.105 r_bond_refined_d 0.043 r_gen_planes_refined 0.016 r_gen_planes_other 0.014 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2866 Nucleic Acid Atoms 321 Solvent Atoms 91 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing