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Structure of human sialyltransferase ST8SiaIII in complex with CDP
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 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.928 α = 90 b = 96.867 β = 90 c = 124.981 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 2.07 58.26 98.9 0.055 0.024 0.999 22.3 6 53860
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 2.07 2.13 95.5 0.649 0.318 0.833 2.7 4.9 3984
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 2.07 58.26 51139 2670 98.41 0.1694 0.1677 0.1767 0.2017 0.2099 RANDOM 39.925
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] 2.12 -0.08 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.169 r_dihedral_angle_4_deg 19.651 r_dihedral_angle_3_deg 15.158 r_dihedral_angle_1_deg 6.42 r_mcangle_it 2.847 r_angle_refined_deg 2.023 r_mcbond_it 1.96 r_mcbond_other 1.945 r_angle_other_deg 1.58 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.169 r_dihedral_angle_4_deg 19.651 r_dihedral_angle_3_deg 15.158 r_dihedral_angle_1_deg 6.42 r_mcangle_it 2.847 r_angle_refined_deg 2.023 r_mcbond_it 1.96 r_mcbond_other 1.945 r_angle_other_deg 1.58 r_chiral_restr 0.132 r_bond_refined_d 0.021 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 4683 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 267
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing XDS data scaling