9IFR | pdb_00009ifr

CLIPPER domain from the Gram-negative fibrillar adhesin "B9T28_05395

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, HANGING DROP		298	5 mg/mL protein, sample buffer: 20 mM Tris, 100 mM NaCl, pH 8.0, crystallization buffer: 0.2 M Ammonium Sulphate, 0.2 M Sodium/Potassium Tartrate, pH 5.5, droplet size 4 microL at 1:1 protein:crystal buffer ratio, with 1mL crystallization buffer in reservoir.

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.859	α = 90
b = 93.859	β = 90
c = 21.994	γ = 120

Symmetry
Space Group	P 63

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		2023-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9795	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.77	81.285	99.91	0.161	0.993	5.1	38.7		11209			26.87

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.8	97.16		3.626	0.401	0.4	29.5

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	1.77	81.284	11203	569	99.857	0.201	0.2001	0.1979	0.2094	0.2103	32.452

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]
-0.616	-0.308		-0.616		1.998

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.874
r_dihedral_angle_3_deg	14.201
r_scangle_it	7.148
r_lrange_it	6.858
r_scbond_it	5.642
r_dihedral_angle_1_deg	5.416
r_mcangle_it	3.843
r_mcbond_it	3.515
r_angle_refined_deg	1.544
r_nbtor_refined	0.301
r_xyhbond_nbd_refined	0.269
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.144
r_chiral_restr	0.066
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	871
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2.multiplex	data reduction
xia2.multiplex	data scaling
MOLREP	phasing