☰ Navigation Tabs
SxtA Methyltransferase and decarboxylase didomain in complex with Mn2+ and SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.25 277 12-14mg/mL SxtA MT-DC in 50mM Tris pH7.4, 50mM NaCl, 10%(v/v) glycerol, 5mM S-adenosyl-L-methionine (SAM), and 5mM MnCl2.
Well solution: 5-8% PEG 20K, and 0.1M MES pH 6.25-6.5
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.802 α = 86.44 b = 69.668 β = 83.26 c = 127.608 γ = 83.95
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 16M 2019-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 2.6 42.43 97.8 0.1261 0.995 8.57 3.6 44788 51.19
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 2.6 2.69 94.19 0.696 1.39 3.5
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 6B3A 2.6 42.43 1.96 44788 3931 97.8 0.2402 0.2375 0.2376 0.298 0.2977 64.76
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 11.1916 f_angle_d 0.6514 f_chiral_restr 0.0423 f_plane_restr 0.0051 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10723 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement JBluIce-EPICS data collection XDS data reduction XDS data scaling PHASER phasing