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Crystal structure of human ClpP in complex with ZK53
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TG6 1TG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2M Magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350, pH7.9
Crystal Properties Matthews coefficient Solvent content 2.12 42.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.31 α = 90 b = 97 β = 93.98 c = 123.84 γ = 90
Symmetry Space Group P 1 21 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 2021-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 20.53 99.9 0.11 10.4 6.9 223016
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 1.9 1.95 0.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TG6 1.9 20.53 212014 10975 99.84 0.1874 0.18565 0.22106 0.239 RANDOM 33.321
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] 1.25 2.52 0.64 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.283 r_sphericity_free 39.777 r_dihedral_angle_4_deg 15.187 r_dihedral_angle_3_deg 14.342 r_sphericity_bonded 11.527 r_dihedral_angle_1_deg 5.861 r_long_range_B_refined 4.931 r_long_range_B_other 4.908 r_scangle_other 4.17 r_mcangle_it 3.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.283 r_sphericity_free 39.777 r_dihedral_angle_4_deg 15.187 r_dihedral_angle_3_deg 14.342 r_sphericity_bonded 11.527 r_dihedral_angle_1_deg 5.861 r_long_range_B_refined 4.931 r_long_range_B_other 4.908 r_scangle_other 4.17 r_mcangle_it 3.957 r_mcangle_other 3.957 r_scbond_it 3.604 r_scbond_other 3.601 r_mcbond_it 3.201 r_mcbond_other 3.201 r_rigid_bond_restr 2.346 r_angle_refined_deg 1.329 r_angle_other_deg 0.939 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18933 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 369
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing