8TE9

Crystal Structure of an Isethionate bound Substrate Binding Protein (IseP) from an Isethionate TRAP Transporter

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q312S0-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Sodium nitrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.2	α = 90
b = 83.21	β = 90
c = 91.91	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER X 16M		2023-04-13	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)	R Merge 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	1.25	46.9	98.7	0.102	0.104	0.02	1	23.9	48.5		150942

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27			1.613	1.692	0.504	0.763		21.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.25	46.9	150942	7483	98.592	0.148	0.1465	0.169	18.861

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]
-0.433			0.936		-0.502

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.96
r_dihedral_angle_3_deg	12.46
r_dihedral_angle_2_deg	9.081
r_dihedral_angle_1_deg	6.068
r_lrange_it	5.575
r_lrange_other	5.457
r_scangle_it	4.406
r_scangle_other	4.401
r_scbond_it	3.013
r_scbond_other	2.877
r_mcangle_other	2.069
r_mcangle_it	2.067
r_angle_refined_deg	2.003
r_mcbond_it	1.407
r_mcbond_other	1.404
r_angle_other_deg	0.645
r_nbd_refined	0.229
r_symmetry_nbd_refined	0.198
r_nbd_other	0.198
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.152
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4851
Nucleic Acid Atoms
Solvent Atoms	612
Heterogen Atoms	50

Software

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