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Staphylococcus aureus MazF in complex with nanobody 5
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 8.5 293 0.2 M MgCl2, 0.1 M TRIS pH 8.5, 30% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.32 46.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.6 α = 67.502 b = 50.873 β = 79.804 c = 52.083 γ = 85.349
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 2020-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978 SOLEIL PROXIMA 1
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 1.80048236056 46.9961366314 78.8 0.998 13.55 2.65 34576 23.6616470756
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 1.80048236056 1.91 34.4 0.917 1.78
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 1.80048236056 46.9961366314 1.9613439742 32245 1596 73.7062265704 0.197811004035 0.195452200843 0.1968 0.243854432982 0.2455 35.5688336135
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 14.6007488078 f_angle_d 0.745453338116 f_chiral_restr 0.0520552466107 f_bond_d 0.00443883729132 f_plane_restr 0.00435837058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3540 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing