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Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in a Ternary Complex with Donor Product CMP and Accepter Substrate Lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EX1 PDB ENTRY 2EX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 0.2M lithium sulfate, 30% PEG4000, 0.1M Tris-HCl (pH8.5), VAPOR DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 4.11 70.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.292 α = 90 b = 90.292 β = 90 c = 204.33 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 RIGAKU JUPITER 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.5 50 99.8 0.082 0.082 20 5.4 34277
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.432 0.432 3.7 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2EX1 2.5 41.31 32443 32443 1727 99.84 0.19467 0.19217 0.1903 0.24297 0.2389 RANDOM 44.646
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] -0.2 -0.1 -0.2 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.912 r_dihedral_angle_4_deg 26.286 r_dihedral_angle_3_deg 18.12 r_dihedral_angle_1_deg 14.288 r_scangle_it 2.648 r_angle_refined_deg 1.882 r_scbond_it 1.626 r_mcangle_it 1.196 r_mcbond_it 0.657 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.912 r_dihedral_angle_4_deg 26.286 r_dihedral_angle_3_deg 18.12 r_dihedral_angle_1_deg 14.288 r_scangle_it 2.648 r_angle_refined_deg 1.882 r_scbond_it 1.626 r_mcangle_it 1.196 r_mcbond_it 0.657 r_nbtor_refined 0.316 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.23 r_chiral_restr 0.18 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.157 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3955 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing