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Crystal structure of sliding DNA clamp of Clostridioides difficile
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M HEPES-NaOH pH 7.5, 0.2 M magnesium formate, and 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.899 α = 90 b = 65.233 β = 118.105 c = 81.994 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 S 6M 2021-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.13 48.68 98.7 0.066 0.079 0.997 11.9 3.4 21383
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 98.2 0.608 0.718 0.769 2.2 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.13 41.452 21382 1095 98.453 0.182 0.1786 0.1835 0.2392 0.2423 44.552
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] 0.133 0.015 0.083 -0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.341 r_dihedral_angle_4_deg 22.969 r_dihedral_angle_3_deg 17.367 r_lrange_it 9.161 r_dihedral_angle_1_deg 7.456 r_scangle_it 7.397 r_scbond_it 4.863 r_mcangle_it 4.849 r_mcbond_it 3.323 r_angle_refined_deg 1.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.341 r_dihedral_angle_4_deg 22.969 r_dihedral_angle_3_deg 17.367 r_lrange_it 9.161 r_dihedral_angle_1_deg 7.456 r_scangle_it 7.397 r_scbond_it 4.863 r_mcangle_it 4.849 r_mcbond_it 3.323 r_angle_refined_deg 1.519 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.234 r_symmetry_xyhbond_nbd_refined 0.216 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.119 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2863 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing