☰ Navigation Tabs
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 7j
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.1 M Hepes pH 7.0, 0.2 M Sodium Acetate, 17% PEG 4000, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.375 α = 90 b = 76.405 β = 102.58 c = 128.019 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2019-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.32 29.14 98.4 0.064 0.076 0.041 11.9 3.3 33310 36.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.4 92.6 0.462 0.557 0.309 2.5 3.1
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 7JHK 2.32 29.14 1.33 33164 1619 97.92 0.2627 0.2614 0.2614 0.2874 0.2869 46.94
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 6.2495 f_angle_d 0.7273 f_chiral_restr 0.0453 f_plane_restr 0.0049 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5307 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 176
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing