4X47

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Neu5Ac2en


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293microseeding into 0.8 M NaH2PO4, 1.2M K2HPO4, sodium acetate 0.1M pH 4.5
Crystal Properties
Matthews coefficientSolvent content
2.4149.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.305α = 90
b = 101.305β = 90
c = 131.939γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442014-08-14MSINGLE 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
124599.50.06415.32.933968
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)
122.0399.70.492.61743

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 REPLACEMENTTHROUGHOUT2sli24532166158698.820.21740.21460.2728RANDOM40.44
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]
1.110.561.11-3.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.393
r_dihedral_angle_3_deg16.035
r_dihedral_angle_4_deg12.596
r_dihedral_angle_1_deg7.526
r_mcangle_it4.544
r_mcbond_it3.481
r_mcbond_other3.481
r_angle_refined_deg1.787
r_angle_other_deg0.829
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.393
r_dihedral_angle_3_deg16.035
r_dihedral_angle_4_deg12.596
r_dihedral_angle_1_deg7.526
r_mcangle_it4.544
r_mcbond_it3.481
r_mcbond_other3.481
r_angle_refined_deg1.787
r_angle_other_deg0.829
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms235
Heterogen Atoms25

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building