8J52

Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase mutant D304A in complex with alpha-1,4-galactobiose


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
3.1260.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.499α = 101.922
b = 72.543β = 104.396
c = 81.202γ = 103.708
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2023-03-10MSINGLE 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
11.946.04497.40.0710.1010.0710.9977.83.5113161
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)
11.91.930.5910.6990.4940.7691.6

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-VALUE1.946.044113160558597.4430.1390.13610.192223.858
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]
1.449-0.253-1.6940.2130.206-0.423
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.142
r_dihedral_angle_3_deg14.546
r_dihedral_angle_2_deg9.247
r_dihedral_angle_1_deg6.786
r_rigid_bond_restr5.543
r_lrange_it3.669
r_lrange_other3.581
r_scangle_it3.248
r_scangle_other3.248
r_mcangle_other2.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.142
r_dihedral_angle_3_deg14.546
r_dihedral_angle_2_deg9.247
r_dihedral_angle_1_deg6.786
r_rigid_bond_restr5.543
r_lrange_it3.669
r_lrange_other3.581
r_scangle_it3.248
r_scangle_other3.248
r_mcangle_other2.642
r_mcangle_it2.639
r_scbond_it2.378
r_scbond_other2.378
r_mcbond_it1.949
r_mcbond_other1.948
r_angle_refined_deg1.623
r_angle_other_deg0.566
r_symmetry_nbd_refined0.341
r_nbd_refined0.221
r_nbd_other0.22
r_symmetry_nbd_other0.203
r_nbtor_refined0.186
r_symmetry_xyhbond_nbd_refined0.176
r_xyhbond_nbd_refined0.134
r_chiral_restr0.084
r_symmetry_nbtor_other0.084
r_symmetry_xyhbond_nbd_other0.047
r_bond_refined_d0.013
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 Atoms8091
Nucleic Acid Atoms
Solvent Atoms794
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing