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LID/HID (LMW SLP and HMW SLP interacting domains) from C. difficile (R7404 strain)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.6M sodium citrate tribasic dihidrate
Crystal Properties Matthews coefficient Solvent content 1.86 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.273 α = 90 b = 56.705 β = 122.71 c = 61.813 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 PILATUS 6M 2018-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.5 52.01 98.9 0.047 0.055 0.028 0.998 8.1 3.4 34063 22.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 95.3 0.22 0.27 0.154 0.975 2.6
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 AB INITIO PHASING THROUGHOUT 1.5 52.01 31378 1644 96.55 0.166 0.164 0.1779 0.2045 0.2152 RANDOM 32.518
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] -0.47 0.99 2.4 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_3_deg 12.929 r_dihedral_angle_4_deg 9.263 r_dihedral_angle_1_deg 5.115 r_rigid_bond_restr 1.659 r_angle_refined_deg 1.146 r_angle_other_deg 1.078 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_3_deg 12.929 r_dihedral_angle_4_deg 9.263 r_dihedral_angle_1_deg 5.115 r_rigid_bond_restr 1.659 r_angle_refined_deg 1.146 r_angle_other_deg 1.078 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1709 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction Arcimboldo phasing