9HUA | pdb_00009hua

Glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. 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	3QKW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	289	To produce cocrystals of the UDP complex His6-tagged apo-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9, 150 mM NaCl was incubated with UDP at a final concentration of 1 mM. Crystals formed in 0.1 M Bis-Tris pH 7.5, 0.2 M potassium thiocyanate, 20 % (w/v) PEG 3350 after 14 days

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.406	α = 90
b = 70.687	β = 91.374
c = 140.312	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2021-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9795	Diamond	I24

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	2.6	70.234	99.55	0.2	0.982	5.15	7		43913			49.36

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	2.6	2.693			0.88

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	70.234	43889	2166	99.939	0.228	0.2257	0.2252	0.2761	0.278	70.527

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]
3.169		0.631	-0.556		-2.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.176
r_dihedral_angle_6_deg	14.254
r_dihedral_angle_2_deg	7.836
r_dihedral_angle_1_deg	7.82
r_lrange_it	5.972
r_lrange_other	5.972
r_scangle_it	3.597
r_scangle_other	3.597
r_mcangle_it	2.988
r_mcangle_other	2.988
r_scbond_it	2.216
r_scbond_other	2.216
r_angle_refined_deg	1.826
r_mcbond_it	1.81
r_mcbond_other	1.809
r_angle_other_deg	0.637
r_symmetry_nbd_refined	0.367
r_nbd_other	0.292
r_nbd_refined	0.229
r_symmetry_nbd_other	0.205
r_xyhbond_nbd_refined	0.204
r_nbtor_refined	0.191
r_symmetry_xyhbond_nbd_other	0.181
r_ncsr_local_group_3	0.148
r_ncsr_local_group_6	0.148
r_ncsr_local_group_5	0.145
r_symmetry_xyhbond_nbd_refined	0.125
r_ncsr_local_group_1	0.125
r_ncsr_local_group_4	0.122
r_ncsr_local_group_2	0.106
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.083
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	10569
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing