6OQ5

Structure of the full-length Clostridium difficile toxin B in complex with 3 VHHs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BVL	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental model	PDB	4R04	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental model	PDB	3PEE	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental model	PDB	6C0B	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental model	PDB	3V0A	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental model	PDB	4NP4	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2
experimental model	PDB	4NC2	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M sodium acetate, 0.1M magnesium acetate, and 5% PEG 8K (final pH 5.2)

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.619	α = 90
b = 168.565	β = 90
c = 179.921	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	CCD	ADSC QUANTUM 315		2016-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

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	3.87	48.91	99.4	0.137	7.7	3.7		42971

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	3.87	3.97			1.548

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2	3.87	48.91	40731	2203	99.22	0.26541	0.26275	0.26	0.31516	0.32	RANDOM	169.399

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]
-2.6			2.48		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.591
r_long_range_B_refined	21.701
r_dihedral_angle_4_deg	16.699
r_dihedral_angle_3_deg	15.806
r_mcangle_it	10.572
r_dihedral_angle_1_deg	7.891
r_mcbond_it	6.114
r_scbond_it	5.715
r_angle_refined_deg	1.097
r_chiral_restr	0.093
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21501
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing