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Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP 19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1:1 mixture of reservoir (0.1M Bis-Tris (pH 6.5), 15% PEG3350, 0.2M sodium citrate, 10% ethylene glycol) and protein solution (3.75 mg/mL ClpP1, 3.75 mg/mL ClpP2, 0.83 mM ADEP, 0.83 mM Bz-Leu-Leu, 10 mM HEPES (pH 7.5), 50 mM NaCl, 4.5% DMSO)
Crystal Properties Matthews coefficient Solvent content 2.96 58.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.461 α = 90 b = 183.685 β = 95.337 c = 191.698 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 EIGER X 16M horizontal bounce Si(111) double crystal monochromator 2024-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
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 2.65 50 99.1 0.2 0.227 0.106 0.982 4 4.4 206665 45.61
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 2.65 2.7 98.7 1.47 1.666 0.771 0.42 4.5
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 2.65 41.04 1.33 184802 9248 86.84 0.2016 0.1997 0.1996 0.2374 0.2374 46.02
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 14.3069 f_angle_d 1.1577 f_chiral_restr 0.0706 f_bond_d 0.0111 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39661 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 1528
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction