6S00

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-acetylneuraminic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.8 M sodium formate, 12% PEG 4000, 0.1 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4349.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.262α = 90
b = 79.017β = 94.83
c = 112.935γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.7001DiamondI04

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
1249.751000.2930.3020.0710.99310.31876209
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)
122.041001.9271.9830.4660.7117.7

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 REPLACEMENTTHROUGHOUT6RZD249.872411377999.950.21160.20950.2517RANDOM23.084
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]
0.5-0.460.17-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.437
r_dihedral_angle_4_deg20.689
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg7.453
r_angle_refined_deg1.829
r_angle_other_deg1.366
r_chiral_restr0.213
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.437
r_dihedral_angle_4_deg20.689
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg7.453
r_angle_refined_deg1.829
r_angle_other_deg1.366
r_chiral_restr0.213
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8016
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata collection
Aimlessdata scaling
PHASERphasing
DIALSdata reduction