7AEY

Salmonella typhimurium neuraminidase in complex with isocarba-DANA.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SIL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277Crystals 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 coefficientSolvent content
2.0840.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.089α = 90
b = 81.375β = 90
c = 90.857γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate1998-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.79SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
10.91824.32597.80.070.07819.783.5236859
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)RedundancyNumber Unique Reflections (All)
10.920.94820.3930.5111.971.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3SIL0.91924.3212367621183897.6750.10.09880.11518.866
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]
-0.045-0.2430.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.391
r_dihedral_angle_4_deg15.387
r_dihedral_angle_3_deg13.306
r_dihedral_angle_1_deg8.386
r_mcangle_it7.063
r_mcangle_other7.062
r_lrange_it6.63
r_lrange_other6.173
r_rigid_bond_restr5.706
r_mcbond_other5.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.391
r_dihedral_angle_4_deg15.387
r_dihedral_angle_3_deg13.306
r_dihedral_angle_1_deg8.386
r_mcangle_it7.063
r_mcangle_other7.062
r_lrange_it6.63
r_lrange_other6.173
r_rigid_bond_restr5.706
r_mcbond_other5.139
r_mcbond_it5.138
r_scangle_it3.226
r_scangle_other3.209
r_scbond_it2.569
r_scbond_other2.562
r_angle_refined_deg2.346
r_angle_other_deg1.659
r_symmetry_xyhbond_nbd_refined0.371
r_nbd_refined0.313
r_symmetry_nbd_refined0.294
r_xyhbond_nbd_refined0.258
r_nbd_other0.239
r_symmetry_nbd_other0.199
r_nbtor_refined0.174
r_xyhbond_nbd_other0.146
r_chiral_restr0.14
r_symmetry_nbtor_other0.089
r_symmetry_xyhbond_nbd_other0.064
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2940
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing