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Trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA containing G opposite the crosslink
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 1.8M Ammonium-sulfate, 0.1M sodium-citrate pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.2 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.027 α = 90 b = 77.027 β = 90 c = 164.11 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS EIGER X 9M 2024-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.85 45.38 98.2 0.999 12.8 21.7 42300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 0.168
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 45.38 40131 2080 98.01 0.19582 0.19363 0.2096 0.23671 0.2463 RANDOM 35.405
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] 0.41 0.41 -0.83
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 21.361 r_long_range_B_refined 21.273 r_scangle_other 16.369 r_dihedral_angle_3_deg 12.752 r_mcangle_other 11.328 r_mcangle_it 11.326 r_scbond_other 10.621 r_scbond_it 10.605 r_dihedral_angle_2_deg 7.99 r_mcbond_it 7.778
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 21.361 r_long_range_B_refined 21.273 r_scangle_other 16.369 r_dihedral_angle_3_deg 12.752 r_mcangle_other 11.328 r_mcangle_it 11.326 r_scbond_other 10.621 r_scbond_it 10.605 r_dihedral_angle_2_deg 7.99 r_mcbond_it 7.778 r_mcbond_other 7.768 r_dihedral_angle_1_deg 6.76 r_rigid_bond_restr 4.044 r_angle_refined_deg 1.727 r_angle_other_deg 0.583 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2043 Nucleic Acid Atoms 444 Solvent Atoms 274 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing