4X49

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with oseltamivir carboxylate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2SLI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293micro seeding into 12.5% PEG 3350, 200 mM calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.448.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.097α = 90
b = 101.097β = 90
c = 131.537γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442014-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.0110098.30.06814.22.732612
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.0497.20.4992.41583

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2sli2.0172.8832166150797.460.18710.18410.2452RANDOM30.888
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]
0.650.320.65-2.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.526
r_dihedral_angle_4_deg17.152
r_dihedral_angle_3_deg14.66
r_dihedral_angle_1_deg7.476
r_mcangle_it3.31
r_mcbond_it2.411
r_mcbond_other2.411
r_angle_refined_deg1.802
r_angle_other_deg0.827
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.526
r_dihedral_angle_4_deg17.152
r_dihedral_angle_3_deg14.66
r_dihedral_angle_1_deg7.476
r_mcangle_it3.31
r_mcbond_it2.411
r_mcbond_other2.411
r_angle_refined_deg1.802
r_angle_other_deg0.827
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3803
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms54

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building