7K1U | pdb_00007k1u

Crystal Structure of SrtB-anchored Collagen-binding Adhesin Fragment (residues 206-565) from Clostridioides difficile strain 630

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	Protein: 9.3 mg/ml 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.323	α = 90
b = 69.323	β = 90
c = 187.527	γ = 120

Symmetry
Space Group	P 31 2 1

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	MARMOSAIC 300 mm CCD	BE	2020-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.4	30	100	0.09	0.09	0.096	0.036	0.997	22	7.2		21161		-3	49.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	100		0.834	0.834	0.896	0.326	0.878	1.8	7.4

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	SAD	THROUGHOUT	2.4	29.64	20033	1074	99.81	0.1759	0.1737	0.18	0.2173	0.23	RANDOM	52.26

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]
1.16	0.58		1.16		-3.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.458
r_dihedral_angle_3_deg	9.219
r_dihedral_angle_4_deg	8.687
r_dihedral_angle_1_deg	3.796
r_angle_refined_deg	1.426
r_angle_other_deg	0.345
r_chiral_restr	0.055
r_gen_planes_refined	0.054
r_gen_planes_other	0.052
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.458
r_dihedral_angle_3_deg	9.219
r_dihedral_angle_4_deg	8.687
r_dihedral_angle_1_deg	3.796
r_angle_refined_deg	1.426
r_angle_other_deg	0.345
r_chiral_restr	0.055
r_gen_planes_refined	0.054
r_gen_planes_other	0.052
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1945
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.