8TE9 | pdb_00008te9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.25	46.9	150942	7483	98.592	0.147	0.1461	0.1469	0.1688	0.1696	18.852

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			0.937		-0.505

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.79
r_dihedral_angle_3_deg	12.562
r_dihedral_angle_2_deg	8.314
r_dihedral_angle_1_deg	6.074
r_lrange_it	5.524
r_lrange_other	5.409
r_scangle_it	4.409
r_scangle_other	4.403
r_scbond_it	3.018
r_scbond_other	2.884
r_mcangle_other	2.072
r_mcangle_it	2.071
r_angle_refined_deg	2.014
r_mcbond_it	1.412
r_mcbond_other	1.41
r_angle_other_deg	0.647
r_nbd_refined	0.229
r_nbd_other	0.199
r_symmetry_nbd_refined	0.188
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.15
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.071
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	615
Heterogen Atoms	50

Software

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