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The ligand-bound, open structure of CD0873, a substrate binding protein with adhesive properties from Clostridium difficile.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M MES pH 6.5, with 2% each of PEG 400, 500 MME, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000 and 10,000
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.963 α = 90 b = 57.534 β = 90 c = 148.526 γ = 90
Symmetry Space Group P 21 21 21
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 2018-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.8 74.26 99.9 0.237 0.25 0.077 0.993 7 19.8 31122
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 1.8 1.84 98.3 1.483 1.561 0.483 0.721 1.8 20
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 1.8 74.26 29490 1546 99.96 0.20593 0.20414 0.2119 0.23898 0.2435 RANDOM 30.663
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] 2.69 0.12 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.956 r_dihedral_angle_4_deg 14.866 r_dihedral_angle_3_deg 14.624 r_long_range_B_refined 5.881 r_long_range_B_other 5.865 r_dihedral_angle_1_deg 5.858 r_scangle_other 4.557 r_scbond_it 2.88 r_scbond_other 2.877 r_mcangle_other 2.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.956 r_dihedral_angle_4_deg 14.866 r_dihedral_angle_3_deg 14.624 r_long_range_B_refined 5.881 r_long_range_B_other 5.865 r_dihedral_angle_1_deg 5.858 r_scangle_other 4.557 r_scbond_it 2.88 r_scbond_other 2.877 r_mcangle_other 2.847 r_mcangle_it 2.846 r_mcbond_it 1.904 r_mcbond_other 1.895 r_angle_refined_deg 1.557 r_angle_other_deg 0.934 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2218 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing