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Crystal structure of human ClpP in complex with ZG180
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.2M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.89 α = 90 b = 97.025 β = 93.7 c = 131.42 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 2021-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 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 2.13 54.38 100 0.118 6 6.6 156976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 100 1.231 6.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TG6 2.13 54.33 148823 7770 99.44 0.2318 0.23 0.2418 0.2492 0.2572 RANDOM 51.405
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] -1.2 -1.06 -2.52 3.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.102 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 5.803 r_angle_refined_deg 1.644 r_angle_other_deg 1.008 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.102 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 15.307 r_dihedral_angle_1_deg 5.803 r_angle_refined_deg 1.644 r_angle_other_deg 1.008 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18299 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 519
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing