6Z4Q

Crystal structure of the neurotensin receptor 1 in complex with the small-molecule inverse agonist SR142948A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6.5	293.15	100 mM Bis-Tris 400 mM K citrate 30% (v/v) PEG400 10 uM SR142948A

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.924	α = 90
b = 36.845	β = 113.65
c = 90.288	γ = 90

Symmetry
Space Group	C 1 2 1

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		2018-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.999998	SLS	X06SA

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	2.923	28.307	78.2	0.202	0.225	0.097	0.989	4.7	4.7		8671

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	2.923	3.324	23.9		2.099	2.287	0.895	0.484	1.5	6.4

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	6YVR	2.923	28.307	8669	440	60.335	0.282	0.2806	0.3069	52.98

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]
0.476		-0.153	0.692		-0.747

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.45
r_dihedral_angle_3_deg	14.646
r_dihedral_angle_4_deg	11.687
r_lrange_it	5.78
r_lrange_other	5.779
r_dihedral_angle_1_deg	4.225
r_mcangle_it	1.564
r_mcangle_other	1.564
r_angle_refined_deg	1.186
r_scangle_it	1.135
r_scangle_other	1.134
r_angle_other_deg	1.123
r_mcbond_it	0.863
r_mcbond_other	0.862
r_scbond_it	0.608
r_scbond_other	0.607
r_nbd_refined	0.168
r_nbd_other	0.162
r_nbtor_refined	0.148
r_symmetry_nbd_other	0.147
r_xyhbond_nbd_refined	0.125
r_symmetry_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.079
r_symmetry_nbd_refined	0.078
r_chiral_restr	0.03
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3026
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	50

Software

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