9QC1 | pdb_00009qc1

Crystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist cp28a

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	4.5	293.15	100 mM Na acetate 350 mM K citrate tribasic 30% (v/v) PEG400 50 uM cp28a

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.661	α = 90
b = 215.887	β = 90
c = 95.623	γ = 90

Symmetry
Space Group	C 2 2 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		2023-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.12	107.9	87.8	0.22	0.05	0.99	10.8	25.6		9464

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.12	3.47	43.6		4.7	0.97	0.2	1.4

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	FREE R-VALUE	3.124	107.9	9464	462	66.14	0.301	0.3002	0.3015	0.322	0.3163	83.853

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]
-2.971			1.653		1.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.525
r_dihedral_angle_3_deg	10.648
r_dihedral_angle_2_deg	9.129
r_lrange_it	6.714
r_lrange_other	6.714
r_dihedral_angle_1_deg	4.4
r_mcangle_it	2.694
r_mcangle_other	2.694
r_scangle_it	2.344
r_scangle_other	2.343
r_mcbond_it	1.503
r_mcbond_other	1.502
r_scbond_it	1.294
r_scbond_other	1.294
r_angle_refined_deg	0.9
r_angle_other_deg	0.294
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_refined	0.222
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.176
r_nbd_other	0.167
r_symmetry_nbd_refined	0.16
r_xyhbond_nbd_refined	0.086
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.032
r_chiral_restr_other	0.007
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	3127
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	66

Software

Software
Software Name	Purpose
XDS	data scaling
Aimless	data scaling
Coot	model building
REFMAC	refinement
ISOLDE	model building