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Crystal structure of multifunctional sialyltransferase from pasteurella multocida with CMP-3F-Neu5Ac and alpha-lactose bound
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, HANGING DROP 293 25% PEG MME 2000, 0.2 M NaBr, 40.4% Triton X-100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.482 α = 90 b = 64.532 β = 99.03 c = 64.41 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 BRUKER SMART 6000 2006-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 64.94 99.92 0.0459 10.28 6.18 33299 33274
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.09 100 0.2107 2.15
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 63.63 33274 31548 1680 99.92 0.21276 0.21049 0.2109 0.25493 0.2541 RANDOM 28.035
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] 0.95 0.52 0.15 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.122 r_dihedral_angle_3_deg 14.294 r_dihedral_angle_4_deg 13.256 r_dihedral_angle_1_deg 5.508 r_scangle_it 2.027 r_scbond_it 1.287 r_angle_refined_deg 1.177 r_mcangle_it 0.801 r_mcbond_it 0.51 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.122 r_dihedral_angle_3_deg 14.294 r_dihedral_angle_4_deg 13.256 r_dihedral_angle_1_deg 5.508 r_scangle_it 2.027 r_scbond_it 1.287 r_angle_refined_deg 1.177 r_mcangle_it 0.801 r_mcbond_it 0.51 r_nbtor_refined 0.308 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 3098 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection PROTEUM PLUS data reduction PROTEUM PLUS data scaling AMoRE phasing