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Structure of a bacterial polysialyltransferase in complex with fondaparinux
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 17% - 24% PEG3350 (v/v), 140 - 250 mM Mg2SO4 and 100 mM MES pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.312 α = 90 b = 78.312 β = 90 c = 299.895 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 315r 2015-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.00635 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.1 44.93 100 0.137 0.148 0.054 0.998 14.7 7.2 20333
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.31 100 1.392 1.497 0.545 0.586 7.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.1 44.93 19333 938 99.9 0.1896 0.18725 0.1951 0.23837 0.2429 RANDOM 88.079
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] -0.83 -0.42 -0.83 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.691 r_dihedral_angle_3_deg 18.645 r_dihedral_angle_4_deg 17.464 r_long_range_B_refined 15.065 r_long_range_B_other 15.065 r_scangle_other 9.998 r_mcangle_it 9.3 r_mcangle_other 9.299 r_dihedral_angle_1_deg 6.602 r_scbond_it 6.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.691 r_dihedral_angle_3_deg 18.645 r_dihedral_angle_4_deg 17.464 r_long_range_B_refined 15.065 r_long_range_B_other 15.065 r_scangle_other 9.998 r_mcangle_it 9.3 r_mcangle_other 9.299 r_dihedral_angle_1_deg 6.602 r_scbond_it 6.344 r_scbond_other 6.343 r_mcbond_it 6.002 r_mcbond_other 6.002 r_angle_refined_deg 1.603 r_angle_other_deg 0.965 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6380 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing