8BES

Structure of D188A-fructofuranosidase from Rhodotorula dairenensis in complex with fructose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	18% PEG 3350, 0.2 M MgCl2, 0.1M Bis-Tris pH5.5 at 5.1 mg ml-1 concentration in presence of 20 mM fructose, 1:1 rate Cryocooling: Mother liquor solution supplemented with 20 mM fructose and 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.846	α = 90
b = 112.693	β = 104.9
c = 139.617	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M	KB Mirrors	2021-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	ALBA	XALOC

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	1.86	45.74	99.9	0.071	0.078	0.033	0.998	14	5.5		202338

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	100		0.612	0.399	0.833	2.8	5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	8BEQ	1.86	45.74	192198	10109	99.88	0.18566	0.18404	0.21691	RANDOM	26.497

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]
-0.32		-1.13	1.26		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.32
r_dihedral_angle_4_deg	13.109
r_dihedral_angle_3_deg	12.18
r_dihedral_angle_1_deg	7.526
r_long_range_B_refined	4.657
r_long_range_B_other	4.487
r_scangle_other	2.632
r_mcangle_it	2.144
r_mcangle_other	2.144
r_scbond_it	1.72
r_scbond_other	1.72
r_angle_refined_deg	1.363
r_mcbond_it	1.31
r_mcbond_other	1.31
r_angle_other_deg	1.278
r_chiral_restr	0.057
r_gen_planes_refined	0.006
r_bond_refined_d	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16124
Nucleic Acid Atoms
Solvent Atoms	1980
Heterogen Atoms	958

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
REFMAC	phasing