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The ligand-free, open 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 6HNI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M potassium chloride, 7.5% PEG 6000, 7.5% PEG 8,000, 7.5% PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.394 α = 90 b = 62.254 β = 90 c = 146.102 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 PILATUS 6M-F 2017-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 2.5 146.1 95.9 0.158 0.177 0.079 0.998 6.2 8 12793
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 2.5 2.61 80.2 0.673 0.796 0.344 0.782 1.9 7.7
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 6HNI 2.5 73.05 11819 939 95.31 0.25505 0.25054 0.2525 0.31012 0.3004 RANDOM 66.741
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] 6.86 0.44 -7.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.459 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 15.332 r_long_range_B_other 7.572 r_long_range_B_refined 7.57 r_dihedral_angle_1_deg 6.354 r_mcangle_it 5.412 r_mcangle_other 5.41 r_scangle_other 4.726 r_mcbond_it 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.459 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 15.332 r_long_range_B_other 7.572 r_long_range_B_refined 7.57 r_dihedral_angle_1_deg 6.354 r_mcangle_it 5.412 r_mcangle_other 5.41 r_scangle_other 4.726 r_mcbond_it 3.34 r_mcbond_other 3.339 r_scbond_it 2.736 r_scbond_other 2.735 r_angle_refined_deg 1.28 r_angle_other_deg 0.893 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2200 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing