☰ Navigation Tabs
GlfT2 from Nocardia brasiliensis Bound to Galf Trisaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9DTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 6 mg/mL protein, 0.2% Triton X-100, 0.066 M imidazole, 2 mM magnesium chloride, 8.75% w/v PEG1000, 8.75% w/v PEG3350, 8.75% v/v MPD
Crystal Properties Matthews coefficient Solvent content 2.7 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.784 α = 90 b = 204.965 β = 90 c = 294.126 γ = 90
Symmetry Space Group P 21 21 21
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 2023-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 3.2 34.61 94.9 0.135 5.5 5.2 101657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.31 94.73 0.435 0.89 1.6 5.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 3.2 34.61 101657 92.08 0.2006 0.1997 0.2002 0.248 0.249 51.81
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 12.2398 f_angle_d 0.607 f_chiral_restr 0.0427 f_plane_restr 0.0046 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39120 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 459
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing Coot model building