7X87

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VKW

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) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.135	α = 90
b = 71.615	β = 104.894
c = 130.308	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		2017-04-15	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)	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	1.79	47.93	100	0.995	9.4	3.8		138455

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.82	99.7		0.57	1.6	3.6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7VKW	1.79	47.905	138450	6808	99.969	0.168	0.1663	0.2005	17.597

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]
0.01		0.02	-0.011		-0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.082
r_dihedral_angle_4_deg	20.766
r_dihedral_angle_3_deg	14.266
r_dihedral_angle_1_deg	7.004
r_lrange_it	4.822
r_lrange_other	4.822
r_scangle_it	3.625
r_scangle_other	3.625
r_scbond_it	2.283
r_scbond_other	2.283
r_mcangle_it	2.255
r_mcangle_other	2.255
r_angle_refined_deg	1.591
r_mcbond_it	1.518
r_mcbond_other	1.505
r_angle_other_deg	1.381
r_symmetry_nbd_refined	0.35
r_nbd_other	0.3
r_nbd_refined	0.208
r_nbtor_refined	0.177
r_symmetry_nbd_other	0.176
r_xyhbond_nbd_refined	0.15
r_metal_ion_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.119
r_symmetry_metal_ion_refined	0.087
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.049
r_bond_refined_d	0.01
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	11687
Nucleic Acid Atoms
Solvent Atoms	863
Heterogen Atoms	27

Software

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