8TRP | pdb_00008trp

Structure of a HEPES bound TRAP transporter substrate binding protein.

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	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.89	47.454	26109	1371	99.973	0.178	0.1747	0.17	0.2294	0.23	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
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