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Salmonella typhimurium neuraminidase mutant (D100S)
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 41.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.17 α = 90 b = 81.636 β = 90 c = 91.148 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 2001-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.80 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 30.885 98.3 0.999 15 5 186230 6.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.02 96 0.905 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 30.885 186230 9182 98.062 0.101 0.1007 0.101 0.1161 0.1163 9.881
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] 0.338 -0.285 -0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.784 r_dihedral_angle_4_deg 18.27 r_dihedral_angle_3_deg 13.122 r_dihedral_angle_1_deg 8.004 r_rigid_bond_restr 5.215 r_lrange_it 3.01 r_lrange_other 2.59 r_scangle_it 2.561 r_scangle_other 2.554 r_scbond_other 2.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.784 r_dihedral_angle_4_deg 18.27 r_dihedral_angle_3_deg 13.122 r_dihedral_angle_1_deg 8.004 r_rigid_bond_restr 5.215 r_lrange_it 3.01 r_lrange_other 2.59 r_scangle_it 2.561 r_scangle_other 2.554 r_scbond_other 2.535 r_scbond_it 2.532 r_angle_refined_deg 2.381 r_angle_other_deg 1.618 r_mcangle_it 1.589 r_mcangle_other 1.589 r_mcbond_it 1.181 r_mcbond_other 1.18 r_symmetry_nbd_refined 0.394 r_nbd_other 0.372 r_nbd_refined 0.305 r_symmetry_xyhbond_nbd_refined 0.304 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.132 r_symmetry_nbtor_other 0.086 r_xyhbond_nbd_other 0.067 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2937 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling ACORN phasing