☰ Navigation Tabs
The structure of Lactobacillus fermentum 4,6-alpha-Glucanotransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JBE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M imidazole/hydrochloric acid buffer pH 8.5, 0.2 M calcium acetate , 10% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.83 α = 90 b = 106.08 β = 104.832 c = 106.02 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 S 6M 2020-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.43 48.73 99.9 0.993 7.4 6.9 80425 24.4393052473
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 2.43 2.48 0.827
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 5JBE 2.4300227139 48.7263365866 1.34351629258 80232 3842 99.5990317175 0.196616983888 0.193663259612 0.1954 0.256481915017 0.2552 29.2621144871
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 12.6211232222 f_angle_d 0.865703020996 f_chiral_restr 0.049695173049 f_bond_d 0.00708397023956 f_plane_restr 0.00492789732086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13246 Nucleic Acid Atoms Solvent Atoms 1156 Heterogen Atoms 252
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing