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Clostridioides difficile MarR (WP_003434724)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XT8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 3.0 M NaCl, 0.1 M sodium acetate pH 4.5, and 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 4.21 70.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.483 α = 90 b = 69.402 β = 90 c = 95.007 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 210 2023-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 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 95.01 99.9 0.995 30.1 7.2 41080
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 0.781
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 2.5 95.01 38935 2060 99.77 0.21241 0.20997 0.2156 0.26019 0.2641 RANDOM 60.444
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] 2.5 -1.7 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.349 r_dihedral_angle_3_deg 22.016 r_dihedral_angle_4_deg 17.874 r_long_range_B_other 13.24 r_long_range_B_refined 13.234 r_scangle_other 10.475 r_mcangle_it 8.486 r_mcangle_other 8.485 r_dihedral_angle_1_deg 7.239 r_scbond_it 6.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.349 r_dihedral_angle_3_deg 22.016 r_dihedral_angle_4_deg 17.874 r_long_range_B_other 13.24 r_long_range_B_refined 13.234 r_scangle_other 10.475 r_mcangle_it 8.486 r_mcangle_other 8.485 r_dihedral_angle_1_deg 7.239 r_scbond_it 6.9 r_scbond_other 6.899 r_mcbond_it 5.912 r_mcbond_other 5.912 r_angle_refined_deg 2.027 r_angle_other_deg 0.917 r_chiral_restr 0.106 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 4602 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing