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Clostridioides difficile MarR (WP_003434724) with Hg-bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 3.0 M NaCl, 0.1 M sodium acetate pH 4.5, and 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 4.18 70.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.602 α = 90 b = 69.807 β = 116.41 c = 94.659 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 210 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.00765 PAL/PLS 7A (6B, 6C1)
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 2.5 87.41 98.5 0.994 20.6 1.9 37635
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 2.5 2.54 0.704
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.5 87.41 37635 1992 99.26 0.20001 0.19798 0.23843 0.2405 RANDOM 61.855
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] 2.33 0.99 -2.61 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.842 r_dihedral_angle_4_deg 20.785 r_dihedral_angle_3_deg 19.848 r_long_range_B_other 13.566 r_long_range_B_refined 13.557 r_scangle_other 10.438 r_mcangle_it 7.788 r_mcangle_other 7.788 r_dihedral_angle_1_deg 7.339 r_scbond_it 6.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.842 r_dihedral_angle_4_deg 20.785 r_dihedral_angle_3_deg 19.848 r_long_range_B_other 13.566 r_long_range_B_refined 13.557 r_scangle_other 10.438 r_mcangle_it 7.788 r_mcangle_other 7.788 r_dihedral_angle_1_deg 7.339 r_scbond_it 6.904 r_scbond_other 6.903 r_mcbond_it 5.297 r_mcbond_other 5.286 r_angle_refined_deg 2.01 r_angle_other_deg 0.897 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4593 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AutoSol phasing