☰ Navigation Tabs
Crystal structure of S. epidermidis ClpP in complex with tavaborole - soaking
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, HANGING DROP 4.5 293.15 0.1 M NaOAc (pH 4.5), 30 - 40% (v/v) MPD, and 30 - 40 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.922 α = 90 b = 123.522 β = 91.47 c = 127.029 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 PIXEL DECTRIS EIGER X 16M 2023-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.98 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.692 75.314 81.6 0.068 0.074 0.028 13.9 7 265537
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.692 1.803 23.5 1.25 1.346 0.495 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.91 75.25 1.35 222946 1989 98.7 0.2 0.1999 0.2 0.2103 0.2093
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 17.003 f_angle_d 1.151 f_chiral_restr 0.089 f_bond_d 0.014 f_plane_restr 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19096 Nucleic Acid Atoms Solvent Atoms 1356 Heterogen Atoms 210
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing