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Crystal structure of Pasteurella multocida sialyltransferase D141N mutant with CMP 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 7.5 293 25% PEG 3,350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.961 α = 90 b = 64.533 β = 98.85 c = 64.251 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 2006-06-07 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 64.1 99.92 0.0806 6.09 4.65 33560 33533 20.07
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 99.9 0.3162 1.29 4212
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 2.2 63.5 25138 23919 1286 99.97 0.19918 0.19703 0.1944 0.23921 0.2344 RANDOM 21.366
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] 1.13 0.78 -0.21 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.076 r_dihedral_angle_3_deg 14.699 r_dihedral_angle_4_deg 14.346 r_dihedral_angle_1_deg 5.475 r_scangle_it 1.939 r_scbond_it 1.225 r_angle_refined_deg 1.179 r_mcangle_it 0.751 r_mcbond_it 0.482 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.076 r_dihedral_angle_3_deg 14.699 r_dihedral_angle_4_deg 14.346 r_dihedral_angle_1_deg 5.475 r_scangle_it 1.939 r_scbond_it 1.225 r_angle_refined_deg 1.179 r_mcangle_it 0.751 r_mcbond_it 0.482 r_nbtor_refined 0.306 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.085 r_bond_refined_d 0.01 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 3078 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection PROTEUM PLUS data reduction PROTEUM PLUS data scaling AMoRE phasing