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The ligand-bound, closed structure of CD0873, a substrate binding protein with adhesive properties from Clostridium difficile.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M sodium HEPES pH 7.5, 20% (w/v) PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.107 α = 90 b = 42.351 β = 94.76 c = 56.175 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-F 2018-01-19 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 1.35 55.98 99.9 0.297 0.309 0.086 0.997 9.7 25 67816
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 1.35 1.37 98.8 6.455 6.88 2.319 0.327 1.7 17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3LKV 1.35 55.98 65622 2106 99.99 0.14962 0.14849 0.148 0.18547 0.1841 RANDOM 19.074
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] -0.04 2.09 -1.07 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.29 r_sphericity_free 31.765 r_sphericity_bonded 14.604 r_dihedral_angle_3_deg 11.128 r_dihedral_angle_1_deg 5.505 r_long_range_B_refined 3.801 r_long_range_B_other 3.506 r_scangle_other 3.091 r_dihedral_angle_4_deg 2.856 r_scbond_other 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.29 r_sphericity_free 31.765 r_sphericity_bonded 14.604 r_dihedral_angle_3_deg 11.128 r_dihedral_angle_1_deg 5.505 r_long_range_B_refined 3.801 r_long_range_B_other 3.506 r_scangle_other 3.091 r_dihedral_angle_4_deg 2.856 r_scbond_other 2.67 r_scbond_it 2.668 r_rigid_bond_restr 2.659 r_mcangle_it 2.601 r_mcangle_other 2.6 r_mcbond_other 2.018 r_mcbond_it 2.017 r_angle_refined_deg 1.802 r_angle_other_deg 1.046 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2196 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing