Experiment: 3P0G

 3P0G

Structure of a nanobody-stabilized active state of the beta2 adrenoceptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RH1PDB entries 2RH1 and 3DWT
experimental modelPDB 3DWTPDB entries 2RH1 and 3DWT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829336-44% PEG 400, 100 mM Tris pH 8.0, 4% DMSO, 1% 1,2,3-heptanetriol, twin-syringe mixing method, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 236.686α = 90
b = 45.66β = 102.34
c = 71.375γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray78CCDMARMOSAIC 300 mm CCDmirrors2010-03-10MSINGLE WAVELENGTH
21x-ray78CCDMARMOSAIC 300 mm CCDmirrors2010-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B
2SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,23.55094.80.24.93.5930845.69
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.53.5693.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 2RH1 and 3DWT3.53792109370.24280.23540.3083RANDOM79.94
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]
33.17154.32752.9707-36.1422
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion25.21
t_omega_torsion2.57
t_angle_deg1.22
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3211
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms27

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
BUSTERrefinement