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X-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 20% (w/v) PEG 3350, 200mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.43 α = 90 b = 80.47 β = 104.117 c = 48.77 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 IMAGE PLATE RIGAKU RAXIS VII 2021-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.87 19.322 98.5 0.996 9 3.7 29563
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 1.87 1.92 0.761
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 FREE R-VALUE 1.87 19.322 29563 1501 98.497 0.249 0.2472 0.252 0.2868 0.29 21.628
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 0.029 0.036 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.546 r_dihedral_angle_3_deg 17.998 r_dihedral_angle_1_deg 7.549 r_dihedral_angle_4_deg 6.096 r_lrange_it 5.317 r_lrange_other 5.314 r_scangle_it 4.231 r_scangle_other 4.23 r_mcangle_other 2.909 r_mcangle_it 2.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.546 r_dihedral_angle_3_deg 17.998 r_dihedral_angle_1_deg 7.549 r_dihedral_angle_4_deg 6.096 r_lrange_it 5.317 r_lrange_other 5.314 r_scangle_it 4.231 r_scangle_other 4.23 r_mcangle_other 2.909 r_mcangle_it 2.908 r_scbond_it 2.783 r_scbond_other 2.783 r_mcbond_it 2.061 r_mcbond_other 2.054 r_angle_other_deg 1.245 r_angle_refined_deg 1.186 r_nbd_refined 0.205 r_symmetry_nbd_other 0.2 r_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.148 r_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.054 r_gen_planes_refined 0.014 r_bond_refined_d 0.005 r_gen_planes_other 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing