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crystal structure of multifunctional sialyltransferase from Pasteurella multocida with CMP 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 30%, PEG MME 2000, 0.2 M NaBr, 0.4% Triton X-100 soaked in 20 mM alpha-lactose for one hour, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.912 α = 90 b = 63.627 β = 98.36 c = 63.782 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 2006-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
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 2.15 63.63 93.5 0.083 9.6 2.3 25036 31.564
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 2.15 2.21 95.3 0.381 2.1 2.3 4378
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 2EX1 2.27 63.12 20108 1088 92.78 0.21911 0.21695 0.2136 0.25725 0.2529 RANDOM 32.434
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] 2.85 -0.26 -0.17 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.724 r_dihedral_angle_4_deg 17.955 r_dihedral_angle_3_deg 17.657 r_dihedral_angle_1_deg 5.917 r_scangle_it 2.193 r_scbond_it 1.466 r_angle_refined_deg 1.402 r_mcangle_it 1.011 r_mcbond_it 0.599 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.724 r_dihedral_angle_4_deg 17.955 r_dihedral_angle_3_deg 17.657 r_dihedral_angle_1_deg 5.917 r_scangle_it 2.193 r_scbond_it 1.466 r_angle_refined_deg 1.402 r_mcangle_it 1.011 r_mcbond_it 0.599 r_nbtor_refined 0.31 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.092 r_bond_refined_d 0.012 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 3108 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction SCALA data scaling AMoRE phasing