8FHA | pdb_00008fha

Intramolecular ester bond-containing repeat domain 1 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	0.1 M HEPES, 70% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.051	α = 90
b = 104.712	β = 91.81
c = 52.587	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 16M		2022-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95372	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	1.49	48.09	96.6	0.999	10.5	5.9		81829			18.9

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	1.49	1.52	84.8		0.35		5.4

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 (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	1.49	48.027	78050	4090	97.023	0.169	0.1664	0.18	0.2121	0.22	random selection	21.476

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]
0.31		0.098	-0.451		0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.529
r_dihedral_angle_3_deg	11.578
r_dihedral_angle_1_deg	7.182
r_lrange_it	3.138
r_lrange_other	3.127
r_scangle_it	2.813
r_scangle_other	2.812
r_mcangle_it	2.346
r_mcangle_other	2.346
r_scbond_it	2.324
r_scbond_other	2.297
r_mcbond_it	1.839
r_mcbond_other	1.829
r_angle_other_deg	1.338
r_angle_refined_deg	1.309
r_rigid_bond_restr	1.19
r_symmetry_nbd_refined	0.545
r_nbd_refined	0.183
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.148
r_nbd_other	0.142
r_symmetry_xyhbond_nbd_refined	0.122
r_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.054
r_bond_refined_d	0.008
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	4164
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	10

Software

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