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Crystal structure of human ClpP in complex with ZG36
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 289 0.2M sodium bromide, 20% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.24 α = 90 b = 96.08 β = 92.72 c = 127 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 2022-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
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 1.99 30.85 99.1 0.178 13.7 6.4 184458
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 1.99 2.04 1.061
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 1.99 30.85 174891 9417 98.95 0.23253 0.23104 0.2373 0.25974 0.2642 RANDOM 29.89
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] 0.55 -1.09 -0.44 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 15.765 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_1_deg 5.879 r_long_range_B_refined 3.488 r_long_range_B_other 3.459 r_mcangle_it 1.518 r_mcangle_other 1.518 r_scangle_other 1.518 r_angle_refined_deg 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 15.765 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_1_deg 5.879 r_long_range_B_refined 3.488 r_long_range_B_other 3.459 r_mcangle_it 1.518 r_mcangle_other 1.518 r_scangle_other 1.518 r_angle_refined_deg 1.11 r_scbond_it 0.898 r_scbond_other 0.898 r_mcbond_it 0.871 r_mcbond_other 0.871 r_angle_other_deg 0.864 r_chiral_restr 0.06 r_bond_refined_d 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17575 Nucleic Acid Atoms Solvent Atoms 595 Heterogen Atoms 560
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement autoPROC data reduction PHASER phasing