7AF2

Salmonella typhimurium neuraminidase mutant (D62G)


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.
Crystal Properties
Matthews coefficientSolvent content
2.0840.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.914α = 90
b = 81.357β = 90
c = 91.053γ = 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
10.79218.10794.70.0530.06123.613.2355798
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)
10.7920.8170.11.1611.5720.881.8

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-VALUE3SIL0.79218.1023493681753192.9190.1210.12060.131915.115
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.892
r_rigid_bond_restr15.11
r_dihedral_angle_3_deg12.77
r_dihedral_angle_4_deg12.503
r_dihedral_angle_1_deg7.931
r_scbond_it7.005
r_scbond_other7.003
r_lrange_other6.782
r_lrange_it6.76
r_scangle_it5.994
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.892
r_rigid_bond_restr15.11
r_dihedral_angle_3_deg12.77
r_dihedral_angle_4_deg12.503
r_dihedral_angle_1_deg7.931
r_scbond_it7.005
r_scbond_other7.003
r_lrange_other6.782
r_lrange_it6.76
r_scangle_it5.994
r_scangle_other5.993
r_mcangle_it5.883
r_mcangle_other5.882
r_mcbond_other4.911
r_mcbond_it4.909
r_angle_other_deg2.52
r_angle_refined_deg2.468
r_nbd_refined0.291
r_symmetry_xyhbond_nbd_refined0.259
r_symmetry_nbd_other0.232
r_xyhbond_nbd_refined0.222
r_xyhbond_nbd_other0.21
r_symmetry_nbd_refined0.198
r_nbd_other0.189
r_nbtor_refined0.174
r_chiral_restr0.144
r_symmetry_nbtor_other0.089
r_bond_other_d0.035
r_bond_refined_d0.022
r_gen_planes_other0.02
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2936
Nucleic Acid Atoms
Solvent Atoms502
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing