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Structure of a bacterial polysialyltransferase in complex with CDP
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 2.96 58.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.275 α = 90 b = 78.275 β = 90 c = 303.581 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 RAYONIX MX300HE 2015-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.07253 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 45.23 99.9 0.139 0.155 0.067 0.996 8.8 5.2 22618
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 3.18 100 1.062 1.174 0.495 0.576 5.5
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 45.23 21416 1135 99.89 0.19687 0.19383 0.1947 0.25353 0.2543 RANDOM 81.699
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] 0.24 0.12 0.24 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.361 r_dihedral_angle_4_deg 18.829 r_dihedral_angle_3_deg 18.256 r_long_range_B_refined 12.85 r_long_range_B_other 12.823 r_scangle_other 8.857 r_mcangle_it 7.904 r_mcangle_other 7.903 r_scbond_it 5.71 r_scbond_other 5.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.361 r_dihedral_angle_4_deg 18.829 r_dihedral_angle_3_deg 18.256 r_long_range_B_refined 12.85 r_long_range_B_other 12.823 r_scangle_other 8.857 r_mcangle_it 7.904 r_mcangle_other 7.903 r_scbond_it 5.71 r_scbond_other 5.633 r_dihedral_angle_1_deg 5.628 r_mcbond_it 5.218 r_mcbond_other 5.218 r_angle_refined_deg 1.568 r_angle_other_deg 0.958 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 32 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing