☰ Navigation Tabs
Structure of human sialyltransferase ST8SiaIII in complex with CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 0.2 M (NH4)3PO4, 50 mM PIPES, 18-22% PEG2000
Crystal Properties Matthews coefficient Solvent content 2.83 56.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.335 α = 90 b = 96.497 β = 90 c = 124.655 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 CCD RAYONIX MX300HE 2014-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97947 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 46.94 95.8 0.044 0.021 1 21.7 4.9 70613
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 86.9 0.664 0.398 0.745 2.1 3.5 3897
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5BO8 1.85 46.94 67081 3484 95.22 0.1715 0.17 0.179 0.2002 0.2102 RANDOM 35.902
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] 1.63 -0.75 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.053 r_dihedral_angle_3_deg 15.154 r_dihedral_angle_4_deg 13.716 r_dihedral_angle_1_deg 6.545 r_mcangle_it 2.681 r_angle_refined_deg 1.988 r_mcbond_it 1.82 r_mcbond_other 1.817 r_angle_other_deg 1.695 r_chiral_restr 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.053 r_dihedral_angle_3_deg 15.154 r_dihedral_angle_4_deg 13.716 r_dihedral_angle_1_deg 6.545 r_mcangle_it 2.681 r_angle_refined_deg 1.988 r_mcbond_it 1.82 r_mcbond_other 1.817 r_angle_other_deg 1.695 r_chiral_restr 0.159 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.009 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4667 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 278
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing