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Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MZM experimental model PDB 1YC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.01 M Cobalt(II) chloride hexahydrate, 0.1 M MES monohydrate pH 6.5, 1.8 M Ammonium sulfate, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.98 58.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.1 α = 90 b = 102.1 β = 90 c = 101.15 γ = 120
Symmetry Space Group P 31 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 X 16M 2021-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.978 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.4290937208 45.574579877 98.6 0.995 8.14 9.9 8391 107.190656778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4290937208 3.64 0.372
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 3.4290937208 45.574579877 1.35108234315 8382 420 98.4958871915 0.24628427461 0.244334367676 0.2459 0.283114662681 0.2841 109.132728044
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 11.9134854857 f_angle_d 0.830195278492 f_chiral_restr 0.052814820104 f_plane_restr 0.00449526773557 f_bond_d 0.00281292481509
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3415 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing