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Crystal structure of C. difficile HsmR with DNA bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.20 M Ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.935 α = 90 b = 55.407 β = 96.55 c = 65.793 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 6M 2024-12-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 99.9 0.062 0.998 28.1 3.3 23925
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 0.581 0.883
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 2.2 50 22736 1193 99.65 0.18358 0.1807 0.1956 0.23917 0.2404 RANDOM 52.975
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] -0.35 0.17 0.19 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.77 r_dihedral_angle_3_deg 16.258 r_dihedral_angle_4_deg 15.061 r_long_range_B_refined 9.297 r_long_range_B_other 9.245 r_scangle_other 7.227 r_mcangle_other 6.352 r_mcangle_it 6.35 r_dihedral_angle_1_deg 6.346 r_scbond_it 5.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.77 r_dihedral_angle_3_deg 16.258 r_dihedral_angle_4_deg 15.061 r_long_range_B_refined 9.297 r_long_range_B_other 9.245 r_scangle_other 7.227 r_mcangle_other 6.352 r_mcangle_it 6.35 r_dihedral_angle_1_deg 6.346 r_scbond_it 5.224 r_scbond_other 5.004 r_mcbond_it 4.569 r_mcbond_other 4.552 r_angle_refined_deg 1.756 r_angle_other_deg 1.207 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2244 Nucleic Acid Atoms 896 Solvent Atoms 192 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing