4PXF | pdb_00004pxf

Crystal structure of the active G-protein-coupled receptor opsin in complex with the finger-loop peptide derived from the full-length arrestin-1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	3.2 M (NH4)2SO4 in 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 242.622	α = 90
b = 242.622	β = 90
c = 110.216	γ = 120

Symmetry
Space Group	H 3 2

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 PILATUS 6M-F	mirrors	2012-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9791	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.75	40.04	99.6	0.05	0.05	23.1	7.4	32166	32166			70.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.9	99.2		0.944	2	7.3	4645

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	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	3DQB	2.75	40.04	30511	30511	1637	99.66	0.21659	0.21659	0.21476	0.22	0.25075	0.26	RANDOM	84.895

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]
-1.17	-1.17		-1.17		3.79

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	42.816
r_sphericity_free	40.117
r_dihedral_angle_2_deg	36.438
r_scangle_other	19.421
r_long_range_B_refined	19.062
r_long_range_B_other	19.038
r_scbond_it	16.421
r_scbond_other	16.412
r_mcangle_it	16.286
r_mcangle_other	16.284
r_dihedral_angle_3_deg	15.713
r_mcbond_it	13.846
r_mcbond_other	13.834
r_dihedral_angle_4_deg	12.246
r_rigid_bond_restr	6.208
r_dihedral_angle_1_deg	5.104
r_angle_refined_deg	1.187
r_angle_other_deg	0.798
r_chiral_restr	0.154
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2635
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	159

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling