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Yeast DNA polymerase eta in complex with C8-2-acetylaminofluorene containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIH PDB ENTRY 2JIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4MG/ML, 11-14% PEG3350, 0.15-0.2M CACL2
Crystal Properties Matthews coefficient Solvent content 3.04 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.44 α = 90 b = 103.44 β = 90 c = 292.35 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 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 49 98.2 0.11 26.84 13.1 44372 1.5
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 96.5 0.52 5.99 13.6
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 2JIH 2.7 48.76 40624 3592 100 0.224 0.21972 0.2106 0.27219 0.2493 RANDOM 25.494
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.868 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 16.732 r_dihedral_angle_1_deg 5.794 r_scangle_it 2.833 r_scbond_it 1.654 r_angle_refined_deg 1.442 r_mcangle_it 1.217 r_angle_other_deg 0.914 r_mcbond_it 0.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.868 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 16.732 r_dihedral_angle_1_deg 5.794 r_scangle_it 2.833 r_scbond_it 1.654 r_angle_refined_deg 1.442 r_mcangle_it 1.217 r_angle_other_deg 0.914 r_mcbond_it 0.613 r_mcbond_other 0.082 r_chiral_restr 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 824 Solvent Atoms 89 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing