6TVI

Salmonella typhimurium mutant neuraminidase (D100S)+ 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 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 coefficientSolvent content
2.141.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.068α = 90
b = 81.781β = 90
c = 91.065γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152001-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.90SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1121.9699.70.09111.551888806.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.021000.5733.23.5

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-VALUE3SIL121.959188880572299.5880.1190.11840.13328.86
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]
0.026-0.0710.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.851
r_dihedral_angle_4_deg15.512
r_dihedral_angle_3_deg13.16
r_dihedral_angle_1_deg11.068
r_rigid_bond_restr8.239
r_lrange_it3.239
r_lrange_other3.238
r_scangle_it2.97
r_scangle_other2.97
r_dihedral_angle_other_3_deg2.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.851
r_dihedral_angle_4_deg15.512
r_dihedral_angle_3_deg13.16
r_dihedral_angle_1_deg11.068
r_rigid_bond_restr8.239
r_lrange_it3.239
r_lrange_other3.238
r_scangle_it2.97
r_scangle_other2.97
r_dihedral_angle_other_3_deg2.581
r_angle_refined_deg2.28
r_scbond_it2.213
r_scbond_other2.212
r_mcangle_other1.654
r_mcangle_it1.653
r_angle_other_deg1.645
r_mcbond_it1.46
r_mcbond_other1.459
r_symmetry_xyhbond_nbd_other0.3
r_nbd_refined0.287
r_symmetry_nbd_refined0.268
r_nbd_other0.23
r_symmetry_xyhbond_nbd_refined0.215
r_symmetry_nbd_other0.206
r_xyhbond_nbd_refined0.189
r_nbtor_refined0.177
r_chiral_restr0.136
r_symmetry_nbtor_other0.094
r_bond_refined_d0.022
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms487
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing