8TQN | pdb_00008tqn

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

X-RAY DIFFRACTION

---

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	0.2 M Lithium chloride, 0.1 M MES 6.0, 20 % w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.669	α = 90
b = 73.232	β = 90
c = 95.455	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	1.65	47.773	100	0.087	0.092	0.028	0.999	15.9	19.1		37696

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	1.65	1.68			1.654	1.79	0.671	0.764		13

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	1.65	47.773	37634	1908	99.992	0.199	0.1968	0.2	0.237	0.24	34.771

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]
3.982			-1.845		-2.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.845
r_dihedral_angle_3_deg	16.476
r_lrange_it	7.619
r_lrange_other	7.613
r_dihedral_angle_2_deg	7.212
r_scangle_it	6.593
r_scangle_other	6.591
r_dihedral_angle_1_deg	5.471
r_scbond_it	4.294
r_scbond_other	4.292
r_mcangle_it	3.658
r_mcangle_other	3.657
r_mcbond_it	2.922
r_mcbond_other	2.903
r_angle_refined_deg	1.524
r_angle_other_deg	0.49
r_nbd_refined	0.218
r_nbd_other	0.191
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.079
r_symmetry_nbd_refined	0.078
r_chiral_restr	0.074
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2405
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	12

Software

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