6Z4S | pdb_00006z4s

Crystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) in complex with the small molecule inverse agonist SR48692

X-RAY DIFFRACTION

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Serial Crystallography (SX)

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		293.15	100 mM Na citrate 225-460 mM ammonium nitrate 30-32% (v/v) PEG400 1 uM SR48692

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.518	α = 90
b = 77.727	β = 90
c = 158.394	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		2019-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000009	SLS	X06SA

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

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	2.707	29.353	90.6	0.525	0.564	0.198	0.964	4.3	7.3		10475

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	2.707	3.029			4.678	4.929	1.504	0.294	1.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6YVR	2.707	29.353	10474	552	68.408	0.274	0.2727	0.28	0.2889	0.29	38.575

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]
0.315			1.193		-1.508

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.948
r_dihedral_angle_3_deg	15.324
r_dihedral_angle_4_deg	12.63
r_dihedral_angle_1_deg	3.868
r_lrange_other	3.389
r_lrange_it	3.387
r_angle_refined_deg	1.165
r_angle_other_deg	1.08
r_mcangle_it	0.976
r_mcangle_other	0.976
r_scangle_it	0.572
r_scangle_other	0.572
r_mcbond_it	0.523
r_mcbond_other	0.523
r_scbond_it	0.284
r_scbond_other	0.284
r_nbd_refined	0.167
r_nbtor_refined	0.152
r_symmetry_nbd_other	0.145
r_nbd_other	0.135
r_symmetry_xyhbond_nbd_other	0.126
r_symmetry_nbd_refined	0.117
r_xyhbond_nbd_refined	0.115
r_symmetry_xyhbond_nbd_refined	0.091
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.032
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	3288
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

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