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Nucleotide Binding Domain (residues 475-720) of ABC3 transporter permease from Clostridioides difficile strain 630
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292 Protein: 7.6mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3;
Screen: PACT (B10), 0.2M Magnesium chloride, 0.1M MES (pH 6.0), 20% (w/v) PEG6000
Cryo: drop conditions
Crystal Properties Matthews coefficient Solvent content 1.9 35.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.352 α = 90 b = 79.828 β = 90 c = 88.36 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 2021-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97895 APS 21-ID-D
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 0.181 0.181 0.193 0.067 0.993 10.7 8 15239 -3 25.1
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 0.341 0.731 2 8.1
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 29.62 14374 771 99.77 0.199 0.1966 0.2101 0.2437 0.2551 RANDOM 33.853
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] -3.61 1.79 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.513 r_dihedral_angle_4_deg 11.661 r_dihedral_angle_3_deg 9.925 r_dihedral_angle_1_deg 3.665 r_angle_refined_deg 1.535 r_angle_other_deg 0.372 r_chiral_restr 0.067 r_gen_planes_refined 0.056 r_gen_planes_other 0.049 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.513 r_dihedral_angle_4_deg 11.661 r_dihedral_angle_3_deg 9.925 r_dihedral_angle_1_deg 3.665 r_angle_refined_deg 1.535 r_angle_other_deg 0.372 r_chiral_restr 0.067 r_gen_planes_refined 0.056 r_gen_planes_other 0.049 r_bond_refined_d 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1795 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing