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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 = 46.712 α = 90 b = 111.168 β = 90 c = 142.195 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 CCD ADSC CCD TOROIDAL MIRROR 2003-04-12 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 1.7 43.6 92 0.07 14.8 4 82420 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 1.7 1.79 72 0.32 4.4 3.8
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 1.7 87.71 74228 3909 94.8 0.164 0.162 0.1718 0.197 0.2068 RANDOM 19.07
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] 0.45 -0.14 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.694 r_dihedral_angle_4_deg 15.202 r_dihedral_angle_3_deg 12.229 r_dihedral_angle_1_deg 6.553 r_scangle_it 4.632 r_scbond_it 2.948 r_mcangle_it 2.041 r_angle_refined_deg 1.848 r_mcbond_it 1.244 r_angle_other_deg 1.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.694 r_dihedral_angle_4_deg 15.202 r_dihedral_angle_3_deg 12.229 r_dihedral_angle_1_deg 6.553 r_scangle_it 4.632 r_scbond_it 2.948 r_mcangle_it 2.041 r_angle_refined_deg 1.848 r_mcbond_it 1.244 r_angle_other_deg 1.014 r_symmetry_vdw_refined 0.29 r_symmetry_vdw_other 0.283 r_nbd_other 0.202 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.141 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 4531 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing