7VKY

The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophorose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.53	α = 90
b = 71.66	β = 106.02
c = 129.82	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 210		2017-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2	57.14	99.9	0.1	9.4	3.2		307557

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	99.9		0.386		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	2	55.312	97540	4785	99.82	0.168	0.1656	0.204	15.008

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]
		-0.003			0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.445
r_dihedral_angle_4_deg	21.438
r_dihedral_angle_3_deg	14.829
r_dihedral_angle_1_deg	7.184
r_lrange_it	4.159
r_lrange_other	4.159
r_scangle_it	2.994
r_scangle_other	2.993
r_mcangle_it	2.029
r_mcangle_other	2.029
r_scbond_it	1.841
r_scbond_other	1.841
r_angle_refined_deg	1.577
r_angle_other_deg	1.334
r_mcbond_it	1.276
r_mcbond_other	1.276
r_nbd_refined	0.202
r_symmetry_nbd_refined	0.201
r_symmetry_nbd_other	0.177
r_nbd_other	0.177
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.134
r_symmetry_metal_ion_refined	0.119
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.077
r_metal_ion_refined	0.061
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11633
Nucleic Acid Atoms
Solvent Atoms	597
Heterogen Atoms	49

Software

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