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Contribution of the Active Site Aspartic Acid to Catalysis in the Bacterial Neuraminidase from Micromonospora viridifaciens.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUT PDB ENTRY 1EUT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 16 % PEG 3350, 0.2M AMMONIUM CITRATE.
Crystal Properties Matthews coefficient Solvent content 2.8 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.602 α = 90 b = 111.608 β = 90 c = 143.865 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU-MSC OSMIC MIRRORS 2003-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 19.92 89 0.07 6.9 5.6 44697 6
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 1EUT 2.1 87.71 37473 1984 88.1 0.168 0.166 0.1758 0.219 0.2205 RANDOM 23.41
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] -0.58 -0.08 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.218 r_scangle_it 3.541 r_scbond_it 2.356 r_angle_refined_deg 1.773 r_mcangle_it 1.483 r_mcbond_it 0.929 r_angle_other_deg 0.909 r_symmetry_vdw_other 0.312 r_symmetry_vdw_refined 0.293 r_nbd_other 0.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.218 r_scangle_it 3.541 r_scbond_it 2.356 r_angle_refined_deg 1.773 r_mcangle_it 1.483 r_mcbond_it 0.929 r_angle_other_deg 0.909 r_symmetry_vdw_other 0.312 r_symmetry_vdw_refined 0.293 r_nbd_other 0.266 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.104 r_nbtor_other 0.091 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 4531 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing