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Structure of ClpP from Staphylococcus aureus in complex with ZY27
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 0.01 M Iron chloride hexahydate, 0.1 M Sodium citrate tribasic dihydrate, pH 5.6,10% Jeffamine
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.416 α = 90 b = 190.263 β = 117.82 c = 96.201 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 2019-11-28 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) Rrim I (All) Rpim I (All) CC (Half) 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 2.19 95.13 97.9 0.086 0.097 0.044 0.991 7.4 4.2 149067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 95.8 0.29 0.342 0.178 0.801 3.1
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 2.19 95.13 141317 7716 97.51 0.21551 0.21395 0.2172 0.24437 0.245 RANDOM 43.799
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] 0.37 1.79 -2.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.668 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 14.744 r_dihedral_angle_1_deg 5.705 r_long_range_B_refined 3.666 r_long_range_B_other 3.666 r_scangle_other 2.428 r_mcangle_it 2.232 r_mcangle_other 2.232 r_scbond_it 1.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.668 r_dihedral_angle_4_deg 18.114 r_dihedral_angle_3_deg 14.744 r_dihedral_angle_1_deg 5.705 r_long_range_B_refined 3.666 r_long_range_B_other 3.666 r_scangle_other 2.428 r_mcangle_it 2.232 r_mcangle_other 2.232 r_scbond_it 1.394 r_scbond_other 1.394 r_mcbond_it 1.331 r_mcbond_other 1.331 r_angle_refined_deg 1.26 r_angle_other_deg 0.865 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 19979 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 575
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling autoPROC data reduction PHASER phasing