8YVJ | pdb_00008yvj

Crystal structure of the C. difficile toxin A CROPs domain fragment 2592-2710 bound to H5.2 nanobody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F6E
experimental model	PDB	6DBA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288	0.2M Ammonium phosphate dibasic, pH 8.0, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.156	α = 90
b = 71.739	β = 90
c = 93.405	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	RIGAKU HyPix-6000HE		2023-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.65	21.35	98.5	0.03	0.032	0.009	1	54.1	11.1		26488

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68		82.3	0.107	0.121	0.055	0.983		4.6

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 (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	1.65	21.35	25128	1304	98.51	0.15108	0.14871	0.1485	0.19836	0.1988	RANDOM	11.363

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]
0.11			-0.12		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.689
r_dihedral_angle_2_deg	9.175
r_dihedral_angle_1_deg	6.852
r_long_range_B_refined	4.977
r_scbond_it	2.189
r_angle_refined_deg	2.04
r_mcangle_it	1.926
r_mcbond_it	1.196
r_chiral_restr	0.145
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_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	1883
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction
MoRDa	phasing