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Structure of ClpP from Staphylococcus aureus in complex with ZY18
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 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.293 α = 90 b = 127.033 β = 95.43 c = 145.9 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 2019-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.988 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 2.45 145.25 95.6 0.12 0.134 0.058 0.979 4 4.2 121201
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 2.45 2.54 87.9 0.311 0.367 0.189 0.701 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.45 29.68 115029 6156 95.32 0.19628 0.19431 0.23289 0.2122 RANDOM 38.877
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] 3.13 -1.13 -0.37 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.231 r_dihedral_angle_1_deg 6.091 r_long_range_B_refined 6.052 r_long_range_B_other 6.051 r_dihedral_angle_2_deg 5.098 r_scangle_other 4.509 r_mcangle_it 3.342 r_mcangle_other 3.342 r_scbond_it 2.657 r_scbond_other 2.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.231 r_dihedral_angle_1_deg 6.091 r_long_range_B_refined 6.052 r_long_range_B_other 6.051 r_dihedral_angle_2_deg 5.098 r_scangle_other 4.509 r_mcangle_it 3.342 r_mcangle_other 3.342 r_scbond_it 2.657 r_scbond_other 2.657 r_mcbond_it 2.026 r_mcbond_other 2.026 r_angle_refined_deg 1.107 r_angle_other_deg 0.434 r_chiral_restr 0.105 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 19768 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 632
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling autoPROC data reduction PHASER phasing