6Z8N | pdb_00006z8n

Crystal structure of the neurotensin receptor 1 in complex with the small-molecule full agonist SRI-9829

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	6.8	293.15	100 mM HEPES 370-520 mM Na citrate 32% (v/v) PEG400 10 uM SRI-9829

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.665	α = 90
b = 213.971	β = 90
c = 94.052	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	0.999998	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	2.803	29.595	90.4	0.208	0.232	0.099	0.982	5.1	5.2		13189

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	2.803	3.127			1.866	2.05	0.82	0.32	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	2.803	29.595	13154	659	67.623	0.278	0.277	0.28	0.2986	0.31	65.825

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]
0.576			-0.928		0.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.118
r_dihedral_angle_3_deg	13.553
r_dihedral_angle_4_deg	11.921
r_lrange_other	5.866
r_lrange_it	5.863
r_dihedral_angle_1_deg	4.25
r_mcangle_it	1.835
r_mcangle_other	1.835
r_scangle_it	1.29
r_scangle_other	1.289
r_angle_refined_deg	1.169
r_angle_other_deg	1.116
r_mcbond_it	1.008
r_mcbond_other	1.007
r_scbond_it	0.683
r_scbond_other	0.683
r_nbd_refined	0.174
r_nbtor_refined	0.152
r_symmetry_nbd_other	0.15
r_symmetry_xyhbond_nbd_refined	0.149
r_xyhbond_nbd_refined	0.133
r_nbd_other	0.11
r_symmetry_nbd_refined	0.109
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.031
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	3302
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	33

Software

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