6Z4V | pdb_00006z4v

Crystal structure of the neurotensin receptor 1 (NTSR1-H4bmx) in complex with NTS8-13

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 MES 350-450 mM ammonium tartrate 30% (v/v) PEG400 10 uM NTS8-13

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.223	α = 90
b = 77.533	β = 107.219
c = 111.858	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		2019-12-15	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	2.595	29.251	88.9	0.453	0.484	0.165	0.921	4.3	8.5		14177

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	2.595	2.802			2.576	2.76	0.97	0.458	1.5

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	2.595	29.251	14177	723	80.492	0.256	0.2556	0.26	0.2723	0.27	33.074

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]
0.276		-0.547	1.332		-1.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.61
r_dihedral_angle_3_deg	15.596
r_dihedral_angle_4_deg	15.293
r_dihedral_angle_1_deg	5.631
r_lrange_it	5.607
r_lrange_other	5.607
r_mcangle_it	2.061
r_mcangle_other	2.061
r_scangle_it	2.028
r_scangle_other	2.027
r_angle_refined_deg	1.216
r_mcbond_it	1.215
r_mcbond_other	1.214
r_angle_other_deg	1.196
r_scbond_it	1.178
r_scbond_other	1.176
r_symmetry_xyhbond_nbd_refined	0.189
r_nbd_refined	0.188
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.144
r_nbd_other	0.13
r_symmetry_nbd_refined	0.117
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.047
r_symmetry_xyhbond_nbd_other	0.01
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3433
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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