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Crystal Structure Analysis of the Putative Thioether Synthase SgvP Involved in the Tailoring Step of Griseoviridin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y46 PDB ENTRY 2Y46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 277.15 20%(w/v) Polyethylene glycol 3350, 0.2M Potassium sodium tartrate tetrahydrate, 3.0%(v/v) Dimethyl sulfoxide, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 3.87 68.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.05 α = 90 b = 184.05 β = 90 c = 80.32 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77.15 CCD ADSC QUANTUM 315 2012-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979228 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 29.856 99.89 43006 42958 2 3.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 98.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2Y46 2.6 29.856 2.03 42905 42905 2166 100 0.1774 0.1727 0.1706 0.1815 0.2138 0.2208 RANDOM 30.0195
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 13.699 f_angle_d 1.127 f_chiral_restr 0.066 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6091 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 86
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing PHENIX refinement XDS data reduction SCALA data scaling