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Crystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in complex with a covalently linked product Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein sample: 10 - 20 mg/ml in 10mM Hepes (pH 7.5), 0.1M NaCl, 0.3mM TCEP, 3.3mM Triss (pH 7.5), 0.5% beta-octylglucoside, <4% glycerol
Crystal Properties Matthews coefficient Solvent content 2.18 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.482 α = 90 b = 66.556 β = 103.438 c = 93.446 γ = 90
Symmetry Space Group I 1 2 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 R 4M Rigaku Varimax-HF Arc 2018-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 2.25 29.31 95.2 0.148 0.155 0.047 0.997 0.062 3.84 10.8 15213 21.8
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 2.25 2.3 100 0.602 0.632 0.19 0.972 4.4 10.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4PEO 2.25 29.31 1.34 15160 774 99.57 0.2472 0.2455 0.2462 0.2789 0.2781 30.13
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.8006 f_angle_d 1.8346 f_chiral_restr 0.1166 f_bond_d 0.0199 f_plane_restr 0.0106
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2513 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling PHASER phasing