6S0E

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-Acetyl-2,3-dehydro-2-deoxyneuraminic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.2 M potassium bromide, 15% PEG 4000, 0.1 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.3948.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.418α = 90
b = 78.756β = 94.96
c = 112.82γ = 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
11.978.7699.90.170.1980.0990.915487227
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)
11.91.9399.90.5530.6550.3420.7563.8

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 REPLACEMENTTHROUGHOUT6RZD1.964.5882866432899.870.25310.25040.3067RANDOM20.945
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]
2.690.04-1.05-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.063
r_dihedral_angle_4_deg19.733
r_dihedral_angle_3_deg15.4
r_dihedral_angle_1_deg7.626
r_angle_refined_deg1.841
r_angle_other_deg1.319
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.063
r_dihedral_angle_4_deg19.733
r_dihedral_angle_3_deg15.4
r_dihedral_angle_1_deg7.626
r_angle_refined_deg1.841
r_angle_other_deg1.319
r_chiral_restr0.083
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 Atoms8020
Nucleic Acid Atoms
Solvent Atoms490
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing