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The complex structure of SdnG with its analogue of substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289.15 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02M of each alcohol, 0.1M Bicine/Tris pH 8.5, alcohol (0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2- propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol)
Crystal Properties Matthews coefficient Solvent content 2.61 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.96 α = 90 b = 111.21 β = 113.026 c = 81.59 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2022-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
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 2.2 38.52 99.7 0.088 0.105 0.999 14.5 6.8 51083 40.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.6 0.971 0.603 0.682 1.8
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 2.2 30.74 1.35 51066 2527 99.66 0.203 0.2011 0.2016 0.2397 0.2397 48.79
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 13.3104 f_angle_d 0.6461 f_chiral_restr 0.0451 f_plane_restr 0.0046 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6460 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing