8J50

Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1 M sodium chloride, 50 mM MES-NaOH

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.39

Crystal Data

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

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2022-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.9	46.09	96.4	0.079	0.112	0.079	0.995	6.4	3.5		111441

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)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	77.4		0.437	0.618	0.437	0.77	1.5	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	44.415	111440	5490	96.38	0.139	0.1365	0.1808	27.542

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	-0.307	0.92	-1.226	0.392	0.532

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.867
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_2_deg	8.874
r_dihedral_angle_1_deg	7.049
r_rigid_bond_restr	5.015
r_lrange_it	4.088
r_lrange_other	4.027
r_scangle_it	3.642
r_scangle_other	3.642
r_mcangle_other	2.865
r_mcangle_it	2.864
r_scbond_it	2.66
r_scbond_other	2.659
r_mcbond_it	2.148
r_mcbond_other	2.146
r_angle_refined_deg	1.62
r_angle_other_deg	0.557
r_symmetry_nbd_refined	0.3
r_nbd_other	0.252
r_nbd_refined	0.212
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.132
r_xyhbond_nbd_refined	0.131
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8114
Nucleic Acid Atoms
Solvent Atoms	654
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing