Experiment: 9SJ6

Structure of the Clostridioides difficile CspB protease

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M NaCl, 0.1 M Sodium Acetate trihydrate (pH 4.6) and 30% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.909	α = 90
b = 115.726	β = 90
c = 201.69	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 PILATUS 6M		2025-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

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	1.94	49.4	100	0.99	18.8	13.4		88232

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	1.94	1.97			0.888

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.94	49.4	1.35	88145	4529	99.94	0.2203	0.2183	0.2204	0.2576	0.2593

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.295
f_angle_d	1.022
f_chiral_restr	0.069
f_plane_restr	0.011
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8270
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing