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Trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA containing C opposite the crosslink
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB PDB_00001K3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 1.2M Ammonium-sulfate, 0.1M sodium-citrate pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.02 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.72 α = 90 b = 74.72 β = 90 c = 166.859 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 1.75 44.68 99.9 0.999 12.2 23.3 48567
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 1.75 1.78 0.265
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 1.75 44.68 46091 2406 99.82 0.18852 0.18709 0.1964 0.21627 0.224 RANDOM 30.119
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.191 r_long_range_B_refined 8.565 r_long_range_B_other 8.447 r_dihedral_angle_1_deg 6.454 r_dihedral_angle_2_deg 6.127 r_scangle_other 4.45 r_scbond_it 2.924 r_mcangle_it 2.88 r_mcangle_other 2.88 r_scbond_other 2.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.191 r_long_range_B_refined 8.565 r_long_range_B_other 8.447 r_dihedral_angle_1_deg 6.454 r_dihedral_angle_2_deg 6.127 r_scangle_other 4.45 r_scbond_it 2.924 r_mcangle_it 2.88 r_mcangle_other 2.88 r_scbond_other 2.858 r_mcbond_it 1.85 r_mcbond_other 1.844 r_angle_refined_deg 1.837 r_angle_other_deg 0.616 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2043 Nucleic Acid Atoms 467 Solvent Atoms 359 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing