9C6E | pdb_00009c6e

High-resolution structure of bovine (3-367)Arrestin-1 in a pre-activated conformation

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1 M imidazole, 0.1 M MES pH 6.5, 10% PEG 4000, 20% glycerol, 20 mM sodium formate; 20 mM ammonium acetate; 20 mM sodium citrate tribasic dihydrate; 20 mM potassium sodium tartrate tetrahydrate; 20 mM sodium oxamate

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.56	α = 90
b = 74.76	β = 90
c = 79.77	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		2023-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979460	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	50	99.7	0.096	0.999	13.2	15.8		78726

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48			2.874	0.398	1.1

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	FOURIER SYNTHESIS	THROUGHOUT	1.4	42.19	78725	3937	99.707	0.143	0.1406	0.14	0.1798	0.1804	RANDOM	24.644

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]
-1.48			1.975		-0.495

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.213
r_dihedral_angle_3_deg	11.987
r_dihedral_angle_1_deg	7.102
r_dihedral_angle_2_deg	6.403
r_lrange_it	4.594
r_lrange_other	4.362
r_rigid_bond_restr	2.649
r_scangle_it	2.107
r_scangle_other	2.107
r_mcangle_it	2.013
r_mcangle_other	2.013
r_scbond_it	1.503
r_scbond_other	1.503
r_mcbond_it	1.44
r_mcbond_other	1.44
r_angle_refined_deg	1.212
r_angle_other_deg	0.417
r_metal_ion_refined	0.312
r_nbd_refined	0.244
r_symmetry_nbd_other	0.188
r_nbd_other	0.171
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.091
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.06
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2729
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms	12

Software

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