7VL5

The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with n-octyl-beta-D-glucoside

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	42.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.142	α = 90
b = 71.59	β = 106.024
c = 129.914	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		2017-11-21	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	1.93	47.89	100	0.108	8.8	3.8		108358

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	1.93	1.96	100		0.623	1.9	3.8

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	1.93	19.986	108247	5443	99.881	0.172	0.17	0.2125	21.528

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]
			-0.004		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.018
r_dihedral_angle_4_deg	21.505
r_dihedral_angle_3_deg	14.961
r_dihedral_angle_1_deg	7.355
r_lrange_it	4.943
r_lrange_other	4.911
r_scangle_it	3.796
r_scangle_other	3.796
r_mcangle_it	2.466
r_mcangle_other	2.465
r_scbond_it	2.38
r_scbond_other	2.38
r_mcbond_it	1.652
r_mcbond_other	1.652
r_angle_refined_deg	1.539
r_angle_other_deg	1.332
r_nbd_refined	0.199
r_symmetry_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.184
r_nbd_other	0.182
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.142
r_symmetry_metal_ion_refined	0.129
r_symmetry_xyhbond_nbd_other	0.101
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.075
r_metal_ion_refined	0.054
r_bond_refined_d	0.009
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	11651
Nucleic Acid Atoms
Solvent Atoms	760
Heterogen Atoms	41

Software

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