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Structure of ClpP from Staphylococcus aureus (apo, closed state)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM MES, 0.2 M MgAc, 15% MPD
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.19 α = 105.22 b = 99.25 β = 101.27 c = 107.47 γ = 117.7
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 PSI PILATUS 6M 2017-09-12 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 1.9 50 90.3 0.051 9 1.9 215068
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 1.9 2 0.54 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3V5E 1.9 30 204262 10750 87.44 0.1751 0.1728 0.1743 0.217 0.2206 RANDOM 27.5
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] -0.23 -0.92 -0.36 1.17 -0.23 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_sphericity_free 22.025 r_dihedral_angle_4_deg 16.32 r_dihedral_angle_3_deg 14.631 r_sphericity_bonded 8.353 r_dihedral_angle_1_deg 5.426 r_rigid_bond_restr 1.518 r_angle_refined_deg 1.23 r_chiral_restr 0.077 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_sphericity_free 22.025 r_dihedral_angle_4_deg 16.32 r_dihedral_angle_3_deg 14.631 r_sphericity_bonded 8.353 r_dihedral_angle_1_deg 5.426 r_rigid_bond_restr 1.518 r_angle_refined_deg 1.23 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20603 Nucleic Acid Atoms Solvent Atoms 1975 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing