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Structural and mechanism analysis of YunM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Under the condition of 2000 mM ammonium sulfate, 100 mM CAPS/ sodium hydroxide pH 10.5, 200 mM lithium sulfate an initial crystallization condition was identified over 3 weeks and was subsequently optimized to yield well-diffracting crystals. Final optimized conditions for YunM with SAM contained 1800 mM ammonium sulfate, 100 mM CAPS/sodium hydroxide pH 10.4, 100 mM lithium sulfate, and yielded square crystals
Crystal Properties Matthews coefficient Solvent content 3.31 62.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.741 α = 90 b = 107.741 β = 90 c = 109.163 γ = 120
Symmetry Space Group P 63 2 2
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 ADSC QUANTUM 315r 2021-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9792 SSRF BL18U1
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 1.4 50 99.7 0.992 37.4 1.1 73359
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 1.4 1.42 0.836
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 4HH4 1.4 23.33 1.35 73356 3763 99.63 0.2064 0.2058 0.2057 0.2178 0.2171 17.5102
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1874 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling BALBES phasing