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Salmonella typhimurium mutant neuraminidase (D100S)+ 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 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M K2HPO4 to 1.4M 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 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.068 α = 90 b = 81.781 β = 90 c = 91.065 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 QUANTUM 315 2001-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.90 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1 21.96 99.7 0.091 11.5 5 188880 6.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.02 100 0.573 3.2 3.5
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 1 21.959 188880 5722 99.588 0.119 0.1184 0.1184 0.1332 0.1332 8.86
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] 0.026 -0.071 0.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.851 r_dihedral_angle_4_deg 15.512 r_dihedral_angle_3_deg 13.16 r_dihedral_angle_1_deg 11.068 r_rigid_bond_restr 8.239 r_lrange_it 3.239 r_lrange_other 3.238 r_scangle_it 2.97 r_scangle_other 2.97 r_dihedral_angle_other_3_deg 2.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.851 r_dihedral_angle_4_deg 15.512 r_dihedral_angle_3_deg 13.16 r_dihedral_angle_1_deg 11.068 r_rigid_bond_restr 8.239 r_lrange_it 3.239 r_lrange_other 3.238 r_scangle_it 2.97 r_scangle_other 2.97 r_dihedral_angle_other_3_deg 2.581 r_angle_refined_deg 2.28 r_scbond_it 2.213 r_scbond_other 2.212 r_mcangle_other 1.654 r_mcangle_it 1.653 r_angle_other_deg 1.645 r_mcbond_it 1.46 r_mcbond_other 1.459 r_symmetry_xyhbond_nbd_other 0.3 r_nbd_refined 0.287 r_symmetry_nbd_refined 0.268 r_nbd_other 0.23 r_symmetry_xyhbond_nbd_refined 0.215 r_symmetry_nbd_other 0.206 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.177 r_chiral_restr 0.136 r_symmetry_nbtor_other 0.094 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing