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Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine
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 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.535 α = 90 b = 98.535 β = 90 c = 202.354 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 IMAGE PLATE RIGAKU RAXIS IV Confocal 2006-11-21 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 2.2 15 98.9 0.122 13 17.77 30150 19625
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 90.6 0.4 5.1 11.73
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 2.5 15 19625 1046 99.07 0.23671 0.23435 0.2401 0.28284 0.2806 RANDOM 34.125
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] 0.48 0.24 0.48 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.711 r_dihedral_angle_4_deg 20.628 r_dihedral_angle_3_deg 19.237 r_dihedral_angle_1_deg 6.83 r_scangle_it 2.519 r_angle_refined_deg 1.806 r_scbond_it 1.574 r_mcangle_it 0.968 r_mcbond_it 0.516 r_symmetry_vdw_refined 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.711 r_dihedral_angle_4_deg 20.628 r_dihedral_angle_3_deg 19.237 r_dihedral_angle_1_deg 6.83 r_scangle_it 2.519 r_angle_refined_deg 1.806 r_scbond_it 1.574 r_mcangle_it 0.968 r_mcbond_it 0.516 r_symmetry_vdw_refined 0.431 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.301 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.138 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 2896 Nucleic Acid Atoms 310 Solvent Atoms 69 Heterogen Atoms 32
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling