8QEG | pdb_00008qeg

Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AH8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.09 M Na Acetate pH 4.5, 2.7 % PEG Smears Medium, 6.3 % MPD, 0.5 n-octyl-beta-D-Glucoside and 3% D-Trehalose

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.604	α = 90
b = 102.533	β = 90
c = 154.002	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		2022-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

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	1.7	85.35	100	1	22.4	13.7		126840

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	1.7	1.73	100		0.796	1.9	14.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	59.253	126748	6216	99.956	0.162	0.1604	0.1723	0.1881	0.196	RANDOM	32.934

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]
-0.018			0.009		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.032
r_dihedral_angle_3_deg	13.735
r_dihedral_angle_2_deg	11.067
r_lrange_it	7.397
r_lrange_other	7.241
r_dihedral_angle_1_deg	6.575
r_scangle_it	5.546
r_scangle_other	5.546
r_scbond_it	3.832
r_scbond_other	3.832
r_mcangle_it	3.116
r_mcangle_other	3.116
r_mcbond_it	2.302
r_mcbond_other	2.302
r_angle_refined_deg	1.598
r_dihedral_angle_other_2_deg	0.584
r_angle_other_deg	0.554
r_nbd_refined	0.284
r_symmetry_nbd_refined	0.211
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.166
r_nbd_other	0.14
r_chiral_restr_other	0.123
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5697
Nucleic Acid Atoms
Solvent Atoms	802
Heterogen Atoms	128

Software

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