8I2R

Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y in complex with fructose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M0E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	30% (w/v) polyethylene glycol 10000, 0.2 M magnesium chloride, 0.1 M potassium sodium tartrate, 0.1 M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.542	α = 90
b = 81.697	β = 90
c = 99.602	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2018-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.36	47.8	99.7	0.053	0.023	15.6	6.4		95951

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.36	1.43	100		0.48	0.201	3.5	6.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.36	37.82	90892	4669	99.35	0.1627	0.16174	0.18156	RANDOM	17.745

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.081
r_dihedral_angle_4_deg	14.425
r_dihedral_angle_3_deg	11.613
r_dihedral_angle_1_deg	7.288
r_long_range_B_refined	4.281
r_long_range_B_other	4.038
r_scangle_other	2.594
r_angle_other_deg	2.302
r_mcangle_other	1.935
r_mcangle_it	1.932
r_scbond_it	1.666
r_scbond_other	1.665
r_angle_refined_deg	1.521
r_mcbond_it	1.221
r_mcbond_other	1.215
r_chiral_restr	0.072
r_bond_other_d	0.035
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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	3703
Nucleic Acid Atoms
Solvent Atoms	570
Heterogen Atoms	38

Software

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