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Y370G Active Site Mutant of the Sialidase from Micromonospora viridifaciens in complex with beta-Neu5Ac (sialic acid).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W8O PDB ENTRY 1W8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 16 % PEG 3350, 0.2 M SODIUM FLUORIDE., pH 5.00
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.44 α = 90 b = 49.535 β = 101.74 c = 107.041 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 MARRESEARCH MIRRORS 2004-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.79 34.94 87.3 0.09 11.1 2.7 53080 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 1.8 1.9 87.3 0.22 3.1 2.3
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 1W8O 1.8 105.41 43865 2348 87 0.143 0.14 0.1547 0.199 0.2087 RANDOM 13.61
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] 0.84 0.7 0.59 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 16.689 r_dihedral_angle_3_deg 11.976 r_dihedral_angle_1_deg 7.166 r_scangle_it 3.817 r_scbond_it 2.562 r_angle_refined_deg 1.779 r_mcangle_it 1.621 r_mcbond_it 1.02 r_angle_other_deg 0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 16.689 r_dihedral_angle_3_deg 11.976 r_dihedral_angle_1_deg 7.166 r_scangle_it 3.817 r_scbond_it 2.562 r_angle_refined_deg 1.779 r_mcangle_it 1.621 r_mcbond_it 1.02 r_angle_other_deg 0.933 r_symmetry_vdw_other 0.267 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.213 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.189 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.172 r_chiral_restr 0.113 r_nbtor_other 0.086 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 4527 Nucleic Acid Atoms Solvent Atoms 837 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing