8Y2L | pdb_00008y2l

The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BVL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.01M RbCl, 0.01M SrAc2, 0.01M CsAc, 0.01M BaAc2, 0.1M BES, TEA pH7.5, 12.5% PEG4,000, 20% 1,2,6- Hexanetriol

Crystal Properties
Matthews coefficient	Solvent content
5.36	77.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.166	α = 90
b = 268.755	β = 90
c = 194.862	γ = 90

Symmetry
Space Group	C 2 2 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		2022-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95370	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.95	49.15	99.9	0.998	10.2	8.9		36051

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	3.95	4.13			0.743

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	3.95	49.15	36024	1789	99.917	0.247	0.244	0.241	0.3002	0.2954	147.016

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]
2.927			-0.656		-2.271

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.762
r_lrange_it	11.475
r_lrange_other	11.475
r_dihedral_angle_6_deg	9.106
r_mcangle_it	7.592
r_mcangle_other	7.592
r_scangle_it	7.409
r_scangle_other	7.409
r_dihedral_angle_1_deg	5.76
r_mcbond_it	4.413
r_mcbond_other	4.411
r_scbond_it	4.36
r_scbond_other	4.346
r_dihedral_angle_2_deg	3.079
r_angle_refined_deg	0.801
r_angle_other_deg	0.319
r_nbd_refined	0.2
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.17
r_xyhbond_nbd_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.076
r_symmetry_nbtor_other	0.069
r_nbd_other	0.062
r_ncsr_local_group_1	0.052
r_symmetry_nbd_refined	0.05
r_ncsr_local_group_2	0.048
r_ncsr_local_group_3	0.047
r_chiral_restr	0.039
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13251
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	78

Software

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