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Photorhabdus lamondii ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8R03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, 20% PEG 4000, 10% isopropanole
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.07 α = 90 b = 177.94 β = 112.16 c = 102.84 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 2022-04-07 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 2.5 30 97.7 0.082 10.9 3.1 107872
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 2.5 2.6 95.9 0.667 2 2.9
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 2.5 30 102428 5391 97.78 0.18888 0.18652 0.1947 0.23413 0.2374 RANDOM 56.965
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] -0.47 1.58 -3.77 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.92 r_dihedral_angle_3_deg 14.911 r_dihedral_angle_4_deg 11.203 r_dihedral_angle_1_deg 5.842 r_long_range_B_refined 4.216 r_long_range_B_other 4.198 r_mcangle_it 3.189 r_mcangle_other 3.189 r_scangle_other 3.148 r_mcbond_it 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.92 r_dihedral_angle_3_deg 14.911 r_dihedral_angle_4_deg 11.203 r_dihedral_angle_1_deg 5.842 r_long_range_B_refined 4.216 r_long_range_B_other 4.198 r_mcangle_it 3.189 r_mcangle_other 3.189 r_scangle_other 3.148 r_mcbond_it 2.29 r_mcbond_other 2.29 r_scbond_it 2.257 r_scbond_other 2.256 r_angle_refined_deg 1.163 r_angle_other_deg 1.041 r_rigid_bond_restr 0.509 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 20456 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing