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Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine and incoming TTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ALZ 2ALZ minus DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 12-15% PEG MME 5000, 0.2-0.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.643 α = 90 b = 98.643 β = 90 c = 202.231 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 RIGAKU SATURN 92 2007-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.9 14.99 100 0.144 11.8 27.44 13417 13417
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 2.9 3 100 0.323 4 26.36
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 2ALZ minus DNA 2.9 14.99 12753 663 98.93 0.23858 0.23632 0.2499 0.28203 0.236 RANDOM 14.723
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] 0.7 0.35 0.7 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.523 r_dihedral_angle_4_deg 20.935 r_dihedral_angle_3_deg 19.458 r_dihedral_angle_1_deg 6.269 r_scangle_it 1.623 r_angle_refined_deg 1.532 r_scbond_it 0.977 r_mcangle_it 0.714 r_mcbond_it 0.372 r_symmetry_vdw_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.523 r_dihedral_angle_4_deg 20.935 r_dihedral_angle_3_deg 19.458 r_dihedral_angle_1_deg 6.269 r_scangle_it 1.623 r_angle_refined_deg 1.532 r_scbond_it 0.977 r_mcangle_it 0.714 r_mcbond_it 0.372 r_symmetry_vdw_refined 0.337 r_nbtor_refined 0.303 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.118 r_metal_ion_refined 0.02 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_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 2905 Nucleic Acid Atoms 310 Solvent Atoms 69 Heterogen Atoms 6
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling