7RNQ

Holo structure of engineered TrpB, 2B9-H275E, from Pyrococcus furiosus in the extended-open conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AM7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.85	298	13-21% PEG3350, 0.1 M HEPES pH 7.85

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.013	α = 90
b = 82.683	β = 90
c = 322.558	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 9M		2021-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97618	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.1	41	99.5	0.065	0.995	11.7	13.4		89740

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	93.6		0.684	0.818	1.5	12.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FREE R-VALUE	6AM7	2.102	40.003	89651	4501	99.469	0.216	0.2139	0.2478	45.609

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]
1.379			0.651		-2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.33
r_dihedral_angle_3_deg	13.332
r_dihedral_angle_4_deg	11.624
r_dihedral_angle_1_deg	5.897
r_lrange_it	3.828
r_lrange_other	3.797
r_angle_refined_deg	1.165
r_angle_other_deg	1.137
r_mcangle_it	0.349
r_mcangle_other	0.349
r_scangle_it	0.329
r_scangle_other	0.323
r_nbd_other	0.218
r_mcbond_it	0.197
r_mcbond_other	0.197
r_scbond_it	0.193
r_scbond_other	0.187
r_symmetry_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.173
r_symmetry_nbd_other	0.17
r_nbd_refined	0.166
r_nbtor_refined	0.147
r_metal_ion_refined	0.138
r_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11387
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	24

Software

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