9HTX | pdb_00009htx

Glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Apo form.

X-RAY DIFFRACTION

---

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 apo-enzyme crystallisation screening were conducted with the purified His6-tag-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9 200 mM NaCl. Crystals formed in 0.1 M Bis-Tris pH 7.5, 0.2 M potassium thiocyanate, 20% (w/v) polyethylene glycol (PEG) 3350 after 14-days.

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.439	α = 90
b = 140.491	β = 90
c = 145.324	γ = 90

Symmetry
Space Group	P 21 21 21

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	72.768	99.63	0.112	0.997	20.47	20		98062			40.62

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	2.07			0.781

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	72.768	98015	5101	99.922	0.21	0.2072	0.2018	0.2528	0.2484	70.448

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]
-0.597			-3.023		3.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.92
r_dihedral_angle_6_deg	14.987
r_dihedral_angle_2_deg	13.32
r_lrange_other	10.382
r_lrange_it	10.376
r_scangle_it	7.939
r_scangle_other	7.938
r_dihedral_angle_1_deg	7.511
r_mcangle_it	6.276
r_mcangle_other	6.275
r_scbond_it	5.725
r_scbond_other	5.725
r_mcbond_it	4.632
r_mcbond_other	4.632
r_angle_refined_deg	2.248
r_angle_other_deg	0.913
r_symmetry_nbd_refined	0.28
r_symmetry_xyhbond_nbd_refined	0.254
r_nbd_other	0.214
r_nbd_refined	0.206
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.171
r_symmetry_nbd_other	0.168
r_ncsr_local_group_6	0.14
r_ncsr_local_group_2	0.135
r_ncsr_local_group_3	0.132
r_chiral_restr	0.131
r_ncsr_local_group_4	0.127
r_ncsr_local_group_1	0.122
r_ncsr_local_group_5	0.122
r_symmetry_nbtor_other	0.078
r_xyhbond_nbd_other	0.02
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10810
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	26

Software

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