8T9T | pdb_00008t9t

Apo Crystal Structure of a 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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Sodium bromide, Bis-Tris propane, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.925	α = 90
b = 72.997	β = 90
c = 95.24	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		2022-11-08	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	1.48	47.665	100	0.066	0.07	0.021	0.999	25.6	19.8		50754

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	1.48	1.51			0.539	0.566	0.174	0.975		20.5

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	NONE	1.48	47.665	50684	2541	99.984	0.172	0.17	0.18	0.203	0.21	23

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]
1.288			-0.181		-1.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.249
r_dihedral_angle_3_deg	12.445
r_dihedral_angle_2_deg	8.687
r_lrange_it	5.651
r_dihedral_angle_1_deg	5.63
r_lrange_other	5.582
r_scangle_it	4.608
r_scangle_other	4.607
r_scbond_it	3.164
r_scbond_other	3.164
r_mcangle_other	2.329
r_mcangle_it	2.317
r_angle_refined_deg	2.018
r_mcbond_it	1.705
r_mcbond_other	1.701
r_angle_other_deg	0.683
r_nbd_refined	0.255
r_symmetry_nbd_refined	0.247
r_nbd_other	0.236
r_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_other	0.192
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.184
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
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	2404
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing