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Crystal Structure of Pasteurella multocida sialyltransferase M144D mutant with CMP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IHJ PDB ENTRY 2IHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 24% PEG3350, 50 mM sodium chloride, 0.4% Triton X-100, 100 mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.44 α = 90 b = 61.57 β = 114.15 c = 62.58 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 MARMOSAIC 325 mm CCD 2010-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.45 25 98.1 0.034 0.034 19.06 3.6 64577 63327 -3
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 1.45 1.49 98.2 0.455 2.58 3.3 5052
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 2IHJ 1.45 23.93 64577 63327 3230 98.25 0.18842 0.18701 0.196 0.21482 0.2246 RANDOM 25.652
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] -0.64 0.06 0.81 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 5.67 r_scangle_it 3.86 r_scbond_it 2.463 r_mcangle_it 1.457 r_angle_refined_deg 1.429 r_mcbond_it 0.832 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_3_deg 12.576 r_dihedral_angle_1_deg 5.67 r_scangle_it 3.86 r_scbond_it 2.463 r_mcangle_it 1.457 r_angle_refined_deg 1.429 r_mcbond_it 0.832 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3185 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 21
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling