☰ Navigation Tabs
The structure of alpha2,3-sialyltransferase variant 1 from Pasteurella dagmatis in complex with the donor product CMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V2U PDB ENTRY 4V2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.2 MG/ML PROTEIN CONCENTRATION 0.2 M AMMONIUM CHLORIDE, 20% W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.555 α = 90 b = 113.555 β = 90 c = 65.74 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PIXEL 2014-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.18 50 99.3 0.09 9.5 3.2 25784 1.2
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 2.18 2.26 97.7 0.89 1.2 3
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 4V2U 2.18 50 24101 1249 99.98 0.18906 0.18644 0.1957 0.23794 0.2443 RANDOM 47.52
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] 1.01 0.5 1.01 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.18 r_dihedral_angle_3_deg 16.889 r_dihedral_angle_4_deg 13.492 r_dihedral_angle_1_deg 6.909 r_mcangle_it 5.355 r_scbond_it 4.216 r_mcbond_it 3.651 r_mcbond_other 3.647 r_angle_refined_deg 1.679 r_angle_other_deg 0.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.18 r_dihedral_angle_3_deg 16.889 r_dihedral_angle_4_deg 13.492 r_dihedral_angle_1_deg 6.909 r_mcangle_it 5.355 r_scbond_it 4.216 r_mcbond_it 3.651 r_mcbond_other 3.647 r_angle_refined_deg 1.679 r_angle_other_deg 0.831 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_it 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 3230 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing