8TRP

Structure of a HEPES bound TRAP transporter substrate binding protein.

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	0.1 M HEPES pH 7.5, 20% PEG 4000, 10% 2-Propanol

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.588	α = 90
b = 73.208	β = 90
c = 94.818	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		2022-02-22	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	1.89	47.454	100	0.058	0.06	0.016	1	35.7	26.2		26163

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	1.89	1.93			0.471	0.49	0.132	0.982		26

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	1.89	47.454	26109	1371	99.973	0.178	0.1747	0.2294	34.663

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]
2.847			-1.93		-0.917

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.936
r_dihedral_angle_3_deg	14.103
r_dihedral_angle_2_deg	8.444
r_lrange_it	7.701
r_scangle_it	7.033
r_dihedral_angle_1_deg	5.954
r_scbond_it	4.82
r_mcangle_it	3.782
r_mcbond_it	3.029
r_angle_refined_deg	1.961

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.936
r_dihedral_angle_3_deg	14.103
r_dihedral_angle_2_deg	8.444
r_lrange_it	7.701
r_scangle_it	7.033
r_dihedral_angle_1_deg	5.954
r_scbond_it	4.82
r_mcangle_it	3.782
r_mcbond_it	3.029
r_angle_refined_deg	1.961
r_nbtor_refined	0.313
r_symmetry_xyhbond_nbd_refined	0.222
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.202
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.125
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2381
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	23

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.