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The complex structure of SdnG with product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289.15 0.1M MOPSO/bis-tris pH 6.5, 5%(w/v) PEG 20K, 25%(w/v) 1,1,1-tris(hydroxymethyl)propane, 1%(w/v) NDSB 195, 1mM of each Alkali (10mM rubidium chloride, 10mM strontium acetate, 10mM cesium acetate, 10mM barium acetate)
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.87 α = 90 b = 101.23 β = 90 c = 121.42 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 PILATUS 6M 2022-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.33 45.3 99.8 0.058 0.024 0.999 20.5 2 129094 15.47
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 1.33 1.35 0.78 0.895 0.436 0.753 2.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.33 45.3 1.35 129040 6412 99.8 0.1842 0.1829 0.2095 0.2195 21.16
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 15.1141 f_angle_d 1.3958 f_chiral_restr 0.1053 f_plane_restr 0.0137 f_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4293 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing