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Structure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1M sodium citrate pH5.5, 24% PEG 400, 0.28M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 3.66 66.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.29 α = 90 b = 133.29 β = 90 c = 81.76 γ = 120
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 EIGER X 9M Bimorph K-B pair 2018-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.6 66.71 100 0.148 0.153 0.036 0.999 12.2 17.9 25648
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 2.6 2.67 100 1.177 1.211 0.281 0.642 18.3
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 3bxo 2.6 47.15 1.52 25617 1339 99.86 0.2319 0.2309 0.2314 0.2507 0.2538 62.13
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 15.1537 f_angle_d 0.7682 f_chiral_restr 0.0474 f_bond_d 0.0034 f_plane_restr 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3686 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 108
Software Software Software Name Purpose DIALS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction