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Staphylococcus aureus ClpP Y63W in complex with compound 3471
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, 0.02M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.65 53.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.916 α = 90 b = 125.126 β = 95.13 c = 143.7 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 RAYONIX MX300HE 2017-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.17 50 95.1 0.121 0.136 0.062 9.9 4.1 163105
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 2.17 2.21 88.5 0.613 0.72 0.368 0.607 3.5
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 2.17 49.73 154915 8156 93.59 0.2032 0.2019 0.2049 0.2278 0.2305 RANDOM 34.574
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] 0.29 0.58 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.839 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 6.382 r_angle_refined_deg 1.523 r_angle_other_deg 1.455 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.839 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 6.382 r_angle_refined_deg 1.523 r_angle_other_deg 1.455 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19228 Nucleic Acid Atoms Solvent Atoms 968 Heterogen Atoms 532
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction