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crystal structure of multifunctional sialyltransferase from pasteurella multocida with CMP-3F(equatorial)-Neu5Ac bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG MME 2000
0.2 M NaBr
0.4% Triton X-100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.89 α = 90 b = 65.022 β = 98.56 c = 64.795 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2006-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97947 SSRL BL11-1
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 1.9 64.96 91 0.053 0.048 13.5 2 35617 33809
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 1.9 1.95 88.9 0.177 0.204 3.8 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 2EX1 1.9 32.51 33809 1792 90.02 0.17852 0.17714 0.1757 0.20481 0.2035 RANDOM 28.656
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] 0.06 0.09 -0.07 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.13 r_dihedral_angle_3_deg 14.224 r_dihedral_angle_4_deg 12.068 r_dihedral_angle_1_deg 5.571 r_scangle_it 2.878 r_scbond_it 1.864 r_angle_refined_deg 1.302 r_mcangle_it 1.1 r_mcbond_it 0.75 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.13 r_dihedral_angle_3_deg 14.224 r_dihedral_angle_4_deg 12.068 r_dihedral_angle_1_deg 5.571 r_scangle_it 2.878 r_scbond_it 1.864 r_angle_refined_deg 1.302 r_mcangle_it 1.1 r_mcbond_it 0.75 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 3095 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction SCALA data scaling AMoRE phasing