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Salmonella typhimurium neuraminidase in complex with isocarba-DANA.
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. A 2.5mM solution of isocarba-DANA was then soaked into the resultant crystals for 90 minutes at a temperature of 293K.
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.089 α = 90 b = 81.375 β = 90 c = 90.857 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 0.918 24.325 97.8 0.07 0.078 19.78 3.5 236859
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 0.92 0.94 82 0.393 0.511 1.97 1.9
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 0.919 24.321 236762 11838 97.675 0.1 0.0988 0.0987 0.1151 0.115 8.866
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] -0.045 -0.243 0.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.391 r_dihedral_angle_4_deg 15.387 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 8.386 r_mcangle_it 7.063 r_mcangle_other 7.062 r_lrange_it 6.63 r_lrange_other 6.173 r_rigid_bond_restr 5.706 r_mcbond_other 5.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.391 r_dihedral_angle_4_deg 15.387 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_1_deg 8.386 r_mcangle_it 7.063 r_mcangle_other 7.062 r_lrange_it 6.63 r_lrange_other 6.173 r_rigid_bond_restr 5.706 r_mcbond_other 5.139 r_mcbond_it 5.138 r_scangle_it 3.226 r_scangle_other 3.209 r_scbond_it 2.569 r_scbond_other 2.562 r_angle_refined_deg 2.346 r_angle_other_deg 1.659 r_symmetry_xyhbond_nbd_refined 0.371 r_nbd_refined 0.313 r_symmetry_nbd_refined 0.294 r_xyhbond_nbd_refined 0.258 r_nbd_other 0.239 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.174 r_xyhbond_nbd_other 0.146 r_chiral_restr 0.14 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.064 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2940 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing