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Mutagenesis of the Nucleophilic Tyrosine in a Bacterial Sialidase to Phenylalanine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUU PDB ENTRY 1EUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 16 % PEG 3350, 0.2 M AMMONIUM CITRATE, pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.3 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.258 α = 90 b = 143.258 β = 90 c = 160.25 γ = 120
Symmetry Space Group P 32 2 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 CCD TOROIDAL MIRROR 2004-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 57.83 100 0.07 7.4 7.2 110911 6
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 2.1 2.21 100 0.47 1.5 7
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 1EUU 2.1 124.03 105259 5544 100 0.178 0.175 0.1775 0.238 0.2385 RANDOM 29.34
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] -0.81 -0.4 -0.81 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.507 r_dihedral_angle_4_deg 19.651 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_1_deg 7.114 r_scangle_it 3.806 r_scbond_it 2.593 r_angle_refined_deg 1.835 r_mcangle_it 1.448 r_mcbond_it 0.903 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.507 r_dihedral_angle_4_deg 19.651 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_1_deg 7.114 r_scangle_it 3.806 r_scbond_it 2.593 r_angle_refined_deg 1.835 r_mcangle_it 1.448 r_mcbond_it 0.903 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13589 Nucleic Acid Atoms Solvent Atoms 1078 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing