6ZA8 | pdb_00006za8

Crystal structure of the neurotensin receptor 1 in complex with the small-molecule partial agonist RTI-3a

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		293.1	100 mM HEPES 385-550 mM Na citrate 30-32% (v/v) PEG400 10 uM RTI-3a

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.468	α = 90
b = 211.197	β = 90
c = 93.703	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		2018-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99998	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	2.72	29.64	90.4	0.259	0.281	0.106	0.975	5.2	6.5		13577

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	2.72	3.014			2.395	2.571	0.913	0.435

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	2.72	29.64	13561	656	65.072	0.282	0.2815	0.28	0.3001	0.3	50.142

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]
0.908			-0.778		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.019
r_dihedral_angle_3_deg	14.271
r_dihedral_angle_4_deg	13.99
r_lrange_it	5.045
r_lrange_other	5.044
r_dihedral_angle_1_deg	4.388
r_mcangle_it	1.814
r_mcangle_other	1.814
r_scangle_it	1.372
r_scangle_other	1.372
r_angle_refined_deg	1.165
r_angle_other_deg	1.107
r_mcbond_it	1.01
r_mcbond_other	1.008
r_scbond_it	0.745
r_scbond_other	0.744
r_symmetry_xyhbond_nbd_refined	0.244
r_symmetry_nbd_refined	0.18
r_nbd_refined	0.176
r_nbd_other	0.169
r_symmetry_nbd_other	0.167
r_nbtor_refined	0.154
r_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.034
r_bond_refined_d	0.002
r_gen_planes_refined	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	3313
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	37

Software

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