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Structure of yeast DNA polymerase eta in complex with C8-N-acetyl-2- aminoanthracene containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WTF PDB ENTRY 2WTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.6 4MG/ML,11-14% PEG3350, 0.15-0.2M CACL2, 0.1M CTP, pH 7.6
Crystal Properties Matthews coefficient Solvent content 3.04 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.525 α = 90 b = 103.525 β = 90 c = 292.657 γ = 90
Symmetry Space Group P 41 21 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 PIXEL DECTRIS PILATUS 6M 2010-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.7 50 99.9 0.07 23 4.8 44732 2 52.8
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 2.7 2.85 99.8 0.38 6 4.7
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 PDB ENTRY 2WTF 2.7 46.3 42326 2233 99.55 0.21951 0.21713 0.2211 0.26366 0.2553 RANDOM 39.033
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] -0.46 -0.46 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.432 r_dihedral_angle_4_deg 21.076 r_dihedral_angle_3_deg 17.863 r_dihedral_angle_1_deg 5.165 r_scangle_it 2.26 r_angle_other_deg 2.169 r_mcangle_it 1.521 r_angle_refined_deg 1.418 r_scbond_it 1.303 r_mcbond_it 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.432 r_dihedral_angle_4_deg 21.076 r_dihedral_angle_3_deg 17.863 r_dihedral_angle_1_deg 5.165 r_scangle_it 2.26 r_angle_other_deg 2.169 r_mcangle_it 1.521 r_angle_refined_deg 1.418 r_scbond_it 1.303 r_mcbond_it 0.847 r_chiral_restr 0.076 r_mcbond_other 0.038 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8116 Nucleic Acid Atoms 826 Solvent Atoms 103 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing