☰ Navigation Tabs
Staphylococcus aureus ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.0 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OLL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M ammoniumcitrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.85 56.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.62 α = 90 b = 105.74 β = 102.54 c = 150.37 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 2021-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 30 96.1 0.065 12.8 2.9 219187
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 2.1 99 0.624 3.3 3
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 2 30 208176 10957 96.12 0.16169 0.1595 0.1706 0.20291 0.2101 RANDOM 30.57
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] 1.23 -0.13 -0.64 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.817 r_dihedral_angle_4_deg 16.22 r_dihedral_angle_3_deg 13.19 r_dihedral_angle_1_deg 6.129 r_long_range_B_refined 3.778 r_long_range_B_other 3.694 r_scangle_other 3.243 r_scbond_it 2.609 r_scbond_other 2.609 r_mcangle_it 2.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.817 r_dihedral_angle_4_deg 16.22 r_dihedral_angle_3_deg 13.19 r_dihedral_angle_1_deg 6.129 r_long_range_B_refined 3.778 r_long_range_B_other 3.694 r_scangle_other 3.243 r_scbond_it 2.609 r_scbond_other 2.609 r_mcangle_it 2.485 r_mcangle_other 2.485 r_mcbond_it 1.91 r_mcbond_other 1.909 r_angle_refined_deg 1.298 r_angle_other_deg 1.216 r_rigid_bond_restr 1.157 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19968 Nucleic Acid Atoms Solvent Atoms 1323 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing