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Crystal Structure of the NlpC/P60 Peptidase YkfC from Bacillus subtilis with Covalently Bound Dipeptide
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 6.5 277 20% (w/v) PEG 1000
100 mM MES pH 6.5
200 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.25 62.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.253 α = 90 b = 161.377 β = 94.688 c = 75.391 γ = 90
Symmetry Space Group C 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 EIGER2 X 16M 2024-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0336 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 2.343 47.69 98.7 0.09146 0.1028 0.04588 0.997 11.09 4.7 74048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.343 2.427 95.56 1.095 0.5856 0.49 1.31 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.343 47.688 74045 1555 98.728 0.205 0.204 0.2061 0.2456 0.2472 52.105
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] 0.818 0.878 -0.328 -0.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 40.101 r_dihedral_angle_2_deg 31.119 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 16.54 r_lrange_it 9.276 r_lrange_other 9.276 r_scangle_it 7.38 r_scangle_other 7.379 r_dihedral_angle_1_deg 7.247 r_mcangle_it 6.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 40.101 r_dihedral_angle_2_deg 31.119 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 16.54 r_lrange_it 9.276 r_lrange_other 9.276 r_scangle_it 7.38 r_scangle_other 7.379 r_dihedral_angle_1_deg 7.247 r_mcangle_it 6.006 r_mcangle_other 6.006 r_scbond_it 4.941 r_scbond_other 4.937 r_mcbond_it 4.22 r_mcbond_other 4.219 r_angle_other_deg 2.413 r_angle_refined_deg 2.021 r_symmetry_nbd_refined 0.372 r_nbd_other 0.347 r_symmetry_xyhbond_nbd_other 0.286 r_symmetry_nbd_other 0.216 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.111 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.035 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9550 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing