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Structure of the ClpP:ADEP4-complex from Staphylococcus aureus (open 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 7.5 293 3.5 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.52 α = 90 b = 96.52 β = 90 c = 586.82 γ = 120
Symmetry Space Group P 65 2 2
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 2017-11-04 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 2.2 50 95.6 0.092 9.6 4.5 80457
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 2.2 2.3 97.8 0.592 2.4
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 2.2 30 76395 4021 95.79 0.2093 0.2035 0.2078 0.2383 0.2426 RANDOM 41.018
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] 0.9 0.45 0.9 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.396 r_sphericity_free 25.109 r_dihedral_angle_3_deg 14.909 r_dihedral_angle_4_deg 13.639 r_sphericity_bonded 7.463 r_dihedral_angle_1_deg 5.496 r_angle_refined_deg 1.254 r_rigid_bond_restr 0.562 r_chiral_restr 0.069 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.396 r_sphericity_free 25.109 r_dihedral_angle_3_deg 14.909 r_dihedral_angle_4_deg 13.639 r_sphericity_bonded 7.463 r_dihedral_angle_1_deg 5.496 r_angle_refined_deg 1.254 r_rigid_bond_restr 0.562 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10205 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 385
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing