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Staphylococcus aureus MazF in complex with Nanobody 9
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 6.5 293 0.2 M ammoniumsulphate, 0.1 M Na-cacodylate pH 6.5, 30% (w/v) PEG-8000
Crystal Properties Matthews coefficient Solvent content 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.09 α = 90 b = 133.75 β = 90 c = 100.42 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2020-06-25 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 2.89572919242 46.0840534125 93.5 0.99 9.51 4.8 7201 43.425238765
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 2.89572919242 3.07 0.842 2.65
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 2.89572919242 46.0840534125 1.35933942305 7192 360 93.4511434511 0.255352559346 0.252761150504 0.2517 0.303201178834 0.3024 50.9482501898
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 11.4061975687 f_angle_d 0.570554595903 f_chiral_restr 0.0439709526599 f_plane_restr 0.0037171493906 f_bond_d 0.00216512316656
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1822 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing