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Crystal structure of the sialyltransferase CST-II in complex with trisaccharide acceptor and CMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RO8 PDB ENTRY 1RO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 MM HEPES5, PH 7.5, 8% (W/V) POLYETHYLENE GLYCOL 6000, AND 5% (V/V) 2-METHYL-2, 4-PENTANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.665 α = 90 b = 117.665 β = 90 c = 46.604 γ = 90
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 MARRESEARCH VERTICALLY FOCUSSING MIRROR 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 40 99.6 0.08 38.3 6.3 46782 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 96.9 0.37 5 5.6
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 PDB ENTRY 1RO8 1.95 40 44408 2368 99.6 0.16553 0.16389 0.1834 0.19752 0.22 RANDOM 36.496
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] -1.94 -1.94 3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_4_deg 11.218 r_dihedral_angle_1_deg 5.419 r_scangle_it 2.538 r_scbond_it 1.554 r_angle_refined_deg 1.068 r_mcangle_it 0.998 r_angle_other_deg 0.612 r_mcbond_it 0.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_4_deg 11.218 r_dihedral_angle_1_deg 5.419 r_scangle_it 2.538 r_scbond_it 1.554 r_angle_refined_deg 1.068 r_mcangle_it 0.998 r_angle_other_deg 0.612 r_mcbond_it 0.504 r_mcbond_other 0.11 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4077 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing