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Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide
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, HANGING DROP 4.5 291.15 0.1 M NaOAc pH 4.5, 18-35% MPD, and 0.02 M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.74 55.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.562 α = 90 b = 126.131 β = 93.42 c = 145.794 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 CCD MARRESEARCH Mirrors 2013-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
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 2.27 50 97.3 0.067 10.8 4 155067
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 2.27 2.35 90.4 0.302 3.4 14353
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 3STA 2.26 50 153010 1996 97.37 0.1796 0.1791 0.1852 0.2187 0.2195 RANDOM 37.633
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] 0.67 -0.2 -0.34 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 18.821 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_1_deg 6.406 r_angle_refined_deg 1.823 r_angle_other_deg 1.047 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 18.821 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_1_deg 6.406 r_angle_refined_deg 1.823 r_angle_other_deg 1.047 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19078 Nucleic Acid Atoms Solvent Atoms 679 Heterogen Atoms 714
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction MAR345dtb data collection PHASER phasing