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Salmonella typhimurium neuraminidase mutant (D62G)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes.
Crystal Properties Matthews coefficient Solvent content 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.914 α = 90 b = 81.357 β = 90 c = 91.053 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 MAR scanner 345 mm plate 1998-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.79 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 0.792 18.107 94.7 0.053 0.061 23.61 3.2 355798
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.792 0.81 70.1 1.161 1.572 0.88 1.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3SIL 0.792 18.102 349368 17531 92.919 0.121 0.1206 0.12 0.1319 0.1314 15.115
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] 0.408 -0.283 -0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_rigid_bond_restr 15.11 r_dihedral_angle_3_deg 12.77 r_dihedral_angle_4_deg 12.503 r_dihedral_angle_1_deg 7.931 r_scbond_it 7.005 r_scbond_other 7.003 r_lrange_other 6.782 r_lrange_it 6.76 r_scangle_it 5.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_rigid_bond_restr 15.11 r_dihedral_angle_3_deg 12.77 r_dihedral_angle_4_deg 12.503 r_dihedral_angle_1_deg 7.931 r_scbond_it 7.005 r_scbond_other 7.003 r_lrange_other 6.782 r_lrange_it 6.76 r_scangle_it 5.994 r_scangle_other 5.993 r_mcangle_it 5.883 r_mcangle_other 5.882 r_mcbond_other 4.911 r_mcbond_it 4.909 r_angle_other_deg 2.52 r_angle_refined_deg 2.468 r_nbd_refined 0.291 r_symmetry_xyhbond_nbd_refined 0.259 r_symmetry_nbd_other 0.232 r_xyhbond_nbd_refined 0.222 r_xyhbond_nbd_other 0.21 r_symmetry_nbd_refined 0.198 r_nbd_other 0.189 r_nbtor_refined 0.174 r_chiral_restr 0.144 r_symmetry_nbtor_other 0.089 r_bond_other_d 0.035 r_bond_refined_d 0.022 r_gen_planes_other 0.02 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2936 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing