4X6K

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Siastatin B


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293microseeding into 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.1 M CAPS pH 10.5
Crystal Properties
Matthews coefficientSolvent content
2.3246.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.109α = 90
b = 99.109β = 90
c = 131.708γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442014-09-25MSINGLE 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
11.945098.30.06614.53.134757
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)
11.941.9797.70.45831678

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2sli1.9471.91158697.50.17930.1770.225RANDOM27.04
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]
0.540.270.54-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.068
r_dihedral_angle_3_deg13.524
r_dihedral_angle_4_deg12.547
r_dihedral_angle_1_deg7.491
r_mcangle_it2.879
r_mcbond_it2.234
r_mcbond_other2.234
r_angle_refined_deg1.898
r_angle_other_deg0.87
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.068
r_dihedral_angle_3_deg13.524
r_dihedral_angle_4_deg12.547
r_dihedral_angle_1_deg7.491
r_mcangle_it2.879
r_mcbond_it2.234
r_mcbond_other2.234
r_angle_refined_deg1.898
r_angle_other_deg0.87
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3778
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data reduction