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Crystal Structure of the NlpC/P60 Peptidase YkfC C200A Mutant from Bacillus subtilis with Bound Pentapeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% (w/v) PEG 3000
100 mM MES pH 6.5
200 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.23 61.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.473 α = 90 b = 117.947 β = 90 c = 163.23 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2024-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033220 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.72 47.8 99.56 0.2597 0.2698 0.07239 0.997 11.11 13.7 47821 66.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.724 2.822 98.39 3.233 3.352 0.46 0.91 14.3
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 2.72 47.8 1.35 47739 1529 99.54 0.2437 0.2418 0.2432 0.3003 0.2999 70.36
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 20.4443 f_angle_d 0.9442 f_chiral_restr 0.1498 f_plane_restr 0.0058 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9446 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 150
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing