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Crystal structure of Neisseria meningitidis ClpP protease complex with small molecule activator ACP1-06
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1 M sodium acetate,
40% 2-methyl-2,4-pentanediol (MPD)
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.328 α = 90 b = 119.15 β = 90 c = 127.763 γ = 90
Symmetry Space Group P 2 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 CCD RAYONIX MX340-HS 2019-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.0000 APS 14-ID-B
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 1.64 119.15 98.2 0.145 0.16 0.067 0.984 12.1 5.6 179842
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 1.64 1.66 75.1 0.565 0.712 0.426 0.465 2.1
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 THROUGHOUT 6NB1 1.64 97.33 1.38 179770 2010 98.17 0.2378 0.2373 0.2424 0.2816 0.2866 35.0506
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 17.421 f_angle_d 1.282 f_chiral_restr 0.062 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9775 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 101
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing