8F90 | pdb_00008f90

Intramolecular ester bond-containing repeat domain 2 from Suipraoptans intestinalis adhesin

X-RAY DIFFRACTION

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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		291	0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.075	α = 90
b = 90.603	β = 90
c = 89.686	γ = 90

Symmetry
Space Group	P 21 21 2

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 EIGER X 16M		2022-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953739	Australian Synchrotron	MX2

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	1.46	45.301	99.6	0.999	10.6	13.6		114397

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	1.46	1.49	92.2		0.211	1	12.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	45.301	88757	4410	99.972	0.159	0.1572	0.17	0.1981	0.21	random selection	22.769

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]
-0.317			0.135		0.182

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.77
r_dihedral_angle_4_deg	11.711
r_dihedral_angle_3_deg	10.419
r_dihedral_angle_1_deg	7.113
r_lrange_it	2.928
r_lrange_other	2.834
r_scangle_it	2.485
r_scangle_other	2.484
r_scbond_it	2.003
r_scbond_other	2.001
r_mcangle_other	1.883
r_mcangle_it	1.879
r_mcbond_it	1.478
r_mcbond_other	1.447
r_angle_other_deg	1.304
r_angle_refined_deg	1.279
r_rigid_bond_restr	0.984
r_nbd_refined	0.186
r_symmetry_nbd_refined	0.18
r_symmetry_nbd_other	0.171
r_nbd_other	0.157
r_nbtor_refined	0.146
r_xyhbond_nbd_refined	0.111
r_symmetry_xyhbond_nbd_refined	0.089
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4346
Nucleic Acid Atoms
Solvent Atoms	459
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing