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Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ILV PDB ENTRY 2ILV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.3 MG/ML OF PROTEIN INDEX SCREEN CONDITION D9 (0.1M TRIS PH 8.5, 25% W/V POLYETHYLENE GLYCOL 3350)
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.724 α = 90 b = 56.59 β = 111.95 c = 79.542 γ = 90
Symmetry Space Group C 1 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 PIXEL PILATUS 2014-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 PETRA III, DESY P11
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 2.71 45.1 98.8 0.11 10.4 3.3 12618 1.9
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 2.71 2.87 97.3 0.63 1.9 3.2
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 2ILV 2.71 45.11 11987 631 99.03 0.19018 0.1863 0.1927 0.26099 0.2567 RANDOM 46.174
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] -0.89 0.64 -1.78 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.47 r_dihedral_angle_3_deg 18.993 r_dihedral_angle_4_deg 18.976 r_dihedral_angle_1_deg 6.32 r_mcangle_it 5.004 r_scbond_it 3.598 r_mcbond_other 3.248 r_mcbond_it 3.247 r_angle_refined_deg 1.646 r_angle_other_deg 0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.47 r_dihedral_angle_3_deg 18.993 r_dihedral_angle_4_deg 18.976 r_dihedral_angle_1_deg 6.32 r_mcangle_it 5.004 r_scbond_it 3.598 r_mcbond_other 3.248 r_mcbond_it 3.247 r_angle_refined_deg 1.646 r_angle_other_deg 0.818 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 3207 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing