3NYA | pdb_00003nya

Crystal structure of the human beta2 adrenergic receptor in complex with the neutral antagonist alprenolol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D4S	PDB entry 3D4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			293	100 mM Bis-Tris Propane pH 6.6-6.8, 120 mM Na-tartrate, 3% 1,3 butanediol, 25-30% PEG 400, Lipidic Cubic Phase (LCP) Crystallization, temperature 293-295K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.577	α = 90
b = 75.73	β = 90
c = 173.403	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	CCD	MARMOSAIC 300 mm CCD		2009-11-19	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2009-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.16	40	92.1	0.12	6.4	3.02	9724	8952		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	3.16	3.35	88.9		0.448	2.09	2.83	1508

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 (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	PDB entry 3D4S	3.16	37.94	8497	456	92.19	0.23479	0.23188	0.23	0.28962	0.28	RANDOM	58.619

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]
6			-1.64		-4.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.511
r_dihedral_angle_3_deg	15.947
r_dihedral_angle_4_deg	13.891
r_dihedral_angle_1_deg	4.886
r_angle_refined_deg	1.045
r_scangle_it	1.031
r_angle_other_deg	0.837
r_mcangle_it	0.66
r_scbond_it	0.597
r_mcbond_it	0.354
r_chiral_restr	0.057
r_mcbond_other	0.033
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3527
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	74

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling