7PP1 | pdb_00007pp1

Crystal structure of the P2Y12 receptor in complex with the inverse agonist selatogrel.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NTJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		298	0.1 M ammonium formate, 0.1 M sodium cacdylate, pH 6.0-6.5, 25-35% PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.09	α = 90
b = 155.37	β = 111.48
c = 47.31	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 PILATUS3 6M		2019-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.78	78.7	98.9	0.99	18.6	50.8		16554

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.78	2.87	91.6		0.5	0.6

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	4ntj	2.78	45.68	16390	1630	98.967	0.246	0.2418	0.24	0.2857	0.29	87.413

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]
4.695		0.05	-6.221		1.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.361
r_dihedral_angle_3_deg	20.355
r_dihedral_angle_4_deg	13.978
r_lrange_it	11.979
r_scangle_it	7.236
r_mcangle_it	7.187
r_dihedral_angle_1_deg	5.269
r_scbond_it	4.506
r_mcbond_it	4.342
r_angle_refined_deg	0.919

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.361
r_dihedral_angle_3_deg	20.355
r_dihedral_angle_4_deg	13.978
r_lrange_it	11.979
r_scangle_it	7.236
r_mcangle_it	7.187
r_dihedral_angle_1_deg	5.269
r_scbond_it	4.506
r_mcbond_it	4.342
r_angle_refined_deg	0.919
r_nbtor_refined	0.322
r_symmetry_nbd_refined	0.231
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.152
r_xyhbond_nbd_refined	0.106
r_chiral_restr	0.086
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2837
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	71

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.