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Crystal Structure of DUF4097 domain-Containing Protein from Clostridium difficile Strain 630
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3;
Screen: PEGs II (B6), 0.1M HEPES (pH 7.5), 20% (w/v) PEG1500
Cryo: Reservoir
Crystal Properties Matthews coefficient Solvent content 1.9 35.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.814 α = 90 b = 73.033 β = 90 c = 120.136 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 EIGER X 9M 2021-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 30 99.8 0.127 0.127 0.14 0.057 0.996 14.8 5.9 36987 -3 27.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.478 0.703 1.94 6.1
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 SAD THROUGHOUT 2 27.79 34923 1894 99.72 0.20341 0.20094 0.2096 0.24956 0.2548 RANDOM 37.929
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] -3.58 0.43 3.14
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 10.061 r_long_range_B_refined 10.059 r_scangle_other 6.82 r_dihedral_angle_3_deg 6.139 r_scbond_it 4.173 r_scbond_other 4.172 r_mcangle_other 4.167 r_mcangle_it 4.164 r_dihedral_angle_1_deg 3.118 r_mcbond_it 2.6
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 10.061 r_long_range_B_refined 10.059 r_scangle_other 6.82 r_dihedral_angle_3_deg 6.139 r_scbond_it 4.173 r_scbond_other 4.172 r_mcangle_other 4.167 r_mcangle_it 4.164 r_dihedral_angle_1_deg 3.118 r_mcbond_it 2.6 r_mcbond_other 2.598 r_angle_refined_deg 1.39 r_dihedral_angle_2_deg 1.16 r_angle_other_deg 0.445 r_chiral_restr 0.066 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 4426 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing