7VKZ

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

X-RAY DIFFRACTION

---

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
2.14	42.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.658	α = 90
b = 71.646	β = 106.338
c = 129.52	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		2017-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1	Photon Factory	AR-NW12A

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	47.58	100	0.105	15	7.6		96821

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	100		0.498	4.1	7.6

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	43.106	96817	4944	99.987	0.173	0.1713	0.2076	23.007

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]
-0.002		-0.001	-0.001		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.855
r_dihedral_angle_4_deg	20.68
r_dihedral_angle_3_deg	14.897
r_dihedral_angle_1_deg	7.314
r_lrange_it	4.905
r_lrange_other	4.905
r_scangle_it	3.923
r_scangle_other	3.923
r_scbond_it	2.505
r_scbond_other	2.504
r_mcangle_it	2.476
r_mcangle_other	2.476
r_mcbond_it	1.731
r_mcbond_other	1.73
r_angle_refined_deg	1.555
r_angle_other_deg	1.33
r_nbd_refined	0.202
r_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.185
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.168
r_xyhbond_nbd_refined	0.135
r_symmetry_metal_ion_refined	0.111
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.077
r_metal_ion_refined	0.058
r_chiral_restr_other	0.033
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	11626
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	24

Software

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