8XSG | pdb_00008xsg

Crystal structure of the Actinobacillus minor NM305 glucosyltransferase in complex with UDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8XSH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES pH 6.5, 0.2 M sodium formate, 14% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.136	α = 90
b = 43.39	β = 117.44
c = 95.823	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	PIXEL	DECTRIS EIGER X 16M		2022-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00003	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	50	96.7	0.034	1	33	7		32975

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	1.8	1.84			0.989

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8XSH	1.8	42.557	32974	1696	96.339	0.161	0.1584	0.1586	0.2013	0.2017	28.179

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]
0.838		-0.585	-0.417		0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.207
r_dihedral_angle_3_deg	13.248
r_dihedral_angle_2_deg	9.498
r_dihedral_angle_1_deg	6.804
r_lrange_it	4.11
r_lrange_other	4.019
r_rigid_bond_restr	3.981
r_scangle_it	3.21
r_scangle_other	3.21
r_mcangle_other	2.842
r_mcangle_it	2.837
r_scbond_it	2.317
r_scbond_other	2.315
r_mcbond_it	2.055
r_mcbond_other	2.046
r_angle_refined_deg	1.448
r_angle_other_deg	0.515
r_nbd_refined	0.217
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.187
r_symmetry_nbd_refined	0.186
r_xyhbond_nbd_refined	0.142
r_nbd_other	0.142
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2796
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	29

Software

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