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M. tuberculosis ClpC1-NTD complexed with a click chemistry analog of Rufomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CN8 Rufomycin removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 22% PEG 3K
0.2M calcium acetate
0.1M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.16 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.97 α = 90 b = 57.97 β = 90 c = 131.97 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER2 X 16M 2021-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12723 APS 21-ID-D
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 2.56 57.97 100 0.075 0.078 0.023 0.998 16.7 12 13920 71.66
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 2.56 2.67 100 0.67 0.698 0.194 0.96 12.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.56 39.15 0.71 13919 698 99.86 0.261 0.259 0.264 0.2942 0.2969 108.46
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 31.6752 f_angle_d 1.5173 f_chiral_restr 0.0841 f_bond_d 0.0096 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1125 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing