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Structure of ClpP from Staphylococcus aureus in complex with (S)-ZG197
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3STA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2M Sodium chloride, 0.1M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.84 56.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.029 α = 90 b = 125.285 β = 93.78 c = 145.919 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 2021-10-06 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 2.11 145.6 97.6 0.095 11.1 5.3 180268
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 2.11 2.22 0.736
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 3STA 2.11 145.6 180268 9691 97.46 0.1879 0.1871 0.1943 0.2028 0.2088 RANDOM 40.685
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] 0.71 -0.93 0.07 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.822 r_dihedral_angle_4_deg 17.651 r_dihedral_angle_3_deg 14.108 r_dihedral_angle_1_deg 5.655 r_angle_refined_deg 1.447 r_angle_other_deg 0.921 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.822 r_dihedral_angle_4_deg 17.651 r_dihedral_angle_3_deg 14.108 r_dihedral_angle_1_deg 5.655 r_angle_refined_deg 1.447 r_angle_other_deg 0.921 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19518 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms 652
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing