8J50

Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931 M sodium chloride, 50 mM MES-NaOH
Crystal Properties
Matthews coefficientSolvent content
3.1160.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.662α = 101.741
b = 72.364β = 104.955
c = 81.074γ = 103.664
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
11.946.0996.40.0790.1120.0790.9956.43.5111441
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)
11.91.9377.40.4370.6180.4370.771.53.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.944.415111440549096.380.1390.13650.180827.542
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]
-0.168-0.3070.92-1.2260.3920.532
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.867
r_dihedral_angle_3_deg15.159
r_dihedral_angle_2_deg8.874
r_dihedral_angle_1_deg7.049
r_rigid_bond_restr5.015
r_lrange_it4.088
r_lrange_other4.027
r_scangle_it3.642
r_scangle_other3.642
r_mcangle_other2.865
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.867
r_dihedral_angle_3_deg15.159
r_dihedral_angle_2_deg8.874
r_dihedral_angle_1_deg7.049
r_rigid_bond_restr5.015
r_lrange_it4.088
r_lrange_other4.027
r_scangle_it3.642
r_scangle_other3.642
r_mcangle_other2.865
r_mcangle_it2.864
r_scbond_it2.66
r_scbond_other2.659
r_mcbond_it2.148
r_mcbond_other2.146
r_angle_refined_deg1.62
r_angle_other_deg0.557
r_symmetry_nbd_refined0.3
r_nbd_other0.252
r_nbd_refined0.212
r_symmetry_nbd_other0.201
r_nbtor_refined0.186
r_symmetry_xyhbond_nbd_refined0.132
r_xyhbond_nbd_refined0.131
r_symmetry_nbtor_other0.084
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8114
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing