8J51

Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase in complex with galactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62931 M sodium chloride, 50 mM MES-NaOH, pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.0860.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.357α = 101.822
b = 72.371β = 105.114
c = 80.884γ = 103.668
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-06-25MSINGLE 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)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
12.1546.01980.0970.1380.9939.93.577597
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)
12.152.1997.10.4870.6890.4870.7392.13.5

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-VALUE2.1543.69577593394897.9720.1550.1520.222434.168
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]
0.8420.7450.738-0.8280.221-0.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.395
r_dihedral_angle_3_deg15.267
r_dihedral_angle_2_deg9.488
r_dihedral_angle_1_deg7.099
r_lrange_it4.15
r_lrange_other4.11
r_rigid_bond_restr3.81
r_scangle_it3.29
r_scangle_other3.29
r_mcangle_it2.957
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.395
r_dihedral_angle_3_deg15.267
r_dihedral_angle_2_deg9.488
r_dihedral_angle_1_deg7.099
r_lrange_it4.15
r_lrange_other4.11
r_rigid_bond_restr3.81
r_scangle_it3.29
r_scangle_other3.29
r_mcangle_it2.957
r_mcangle_other2.957
r_scbond_it2.292
r_scbond_other2.291
r_mcbond_it2.057
r_mcbond_other2.056
r_angle_refined_deg1.439
r_angle_other_deg0.496
r_symmetry_nbd_refined0.253
r_nbd_other0.23
r_nbd_refined0.208
r_symmetry_nbd_other0.2
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.137
r_symmetry_xyhbond_nbd_refined0.108
r_symmetry_nbtor_other0.082
r_chiral_restr0.067
r_symmetry_xyhbond_nbd_other0.051
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms386
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing