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The crystal structure of a Radical SAM Enzyme BlsE involved in the Biosynthesis of Blasticidin S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VOB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 293 0.1 M MES monohydrate pH 6.07 , 2.8 M NaCl
Crystal Properties Matthews coefficient Solvent content 6.67 81.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.92 α = 90 b = 163.92 β = 90 c = 158.81 γ = 90
Symmetry Space Group I 41 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 PIXEL DECTRIS PILATUS 6M 2020-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.62 27.32 99.9 0.211 0.998 11.1 26.3 32642 72.1936256233
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 2.62 2.69 0.998
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 FREE R-VALUE 7VOB 2.62005420008 27.2212916085 1.34358397052 32642 1536 99.8806646063 0.214761018098 0.213790999671 0.2144 0.234201946906 0.2353 77.7818123831
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 20.5796574479 f_angle_d 0.670048524243 f_chiral_restr 0.0464946438415 f_plane_restr 0.0053947655311 f_bond_d 0.00317421392537
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2549 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing