6S0F

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6RZD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.15 M potassium thiocyanite, 20% PEG 1500, 0.1 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4148.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.661α = 90
b = 78.924β = 94.89
c = 112.992γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12112.5899.90.1620.1880.0930.9565.4475378
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.041000.5760.660.3180.8484.2

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 REPLACEMENTTHROUGHOUT6RZD2112.5871456386799.820.21940.21690.2648RANDOM21.551
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]
3.390.45-1.97-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.334
r_dihedral_angle_4_deg20.088
r_dihedral_angle_3_deg14.715
r_dihedral_angle_1_deg7.812
r_angle_refined_deg1.879
r_angle_other_deg1.328
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.334
r_dihedral_angle_4_deg20.088
r_dihedral_angle_3_deg14.715
r_dihedral_angle_1_deg7.812
r_angle_refined_deg1.879
r_angle_other_deg1.328
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8027
Nucleic Acid Atoms
Solvent Atoms487
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing