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ATP-dependent Clp endopeptidase proteolytic subunit ClpP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291 0.2 M ammonium acetate, 0.1 M tris pH 8.0, PEG 10000
Crystal Properties Matthews coefficient Solvent content 3.27 62.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 252.981 α = 90 b = 273.576 β = 90 c = 249.499 γ = 90
Symmetry Space Group C 2 2 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 2024-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.03 32.73 99.9 0.997 10 13.5 166729
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.03 3.11 0.813
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 MOLECULAR REPLACEMENT THROUGHOUT 3.03 32.73 157723 8375 99.45 0.2167 0.21502 0.2173 0.2481 0.2496 RANDOM 75.894
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] 2.93 -6.91 3.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.733 r_dihedral_angle_4_deg 20.146 r_dihedral_angle_3_deg 15.816 r_long_range_B_other 14.084 r_long_range_B_refined 14.082 r_scangle_other 10.016 r_mcangle_it 8.899 r_mcangle_other 8.898 r_scbond_it 6.529 r_scbond_other 6.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.733 r_dihedral_angle_4_deg 20.146 r_dihedral_angle_3_deg 15.816 r_long_range_B_other 14.084 r_long_range_B_refined 14.082 r_scangle_other 10.016 r_mcangle_it 8.899 r_mcangle_other 8.898 r_scbond_it 6.529 r_scbond_other 6.529 r_mcbond_it 5.878 r_mcbond_other 5.878 r_dihedral_angle_1_deg 5.856 r_angle_refined_deg 1.421 r_angle_other_deg 1.244 r_chiral_restr 0.059 r_bond_refined_d 0.007 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 39874 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing