3C51

Crystal structure of G protein coupled receptor kinase 1 bound to ADP and magnesium chloride at 3.55A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C4ZPDB ENTRY 3C4Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.25277PEG 8000, NaBr, glycerol, MES pH 6.25, ADP pH 7.5, magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8657.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.657α = 90
b = 92.527β = 90
c = 259.383γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97934APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.553017511

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3C4Z3.5519.881729997.730.281050.28105115.622
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]
0.060.01-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.254
r_dihedral_angle_3_deg18.168
r_dihedral_angle_4_deg15.017
r_dihedral_angle_1_deg5.467
r_scangle_it2.065
r_scbond_it1.411
r_angle_refined_deg1.071
r_angle_other_deg0.809
r_mcangle_it0.77
r_mcbond_it0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.254
r_dihedral_angle_3_deg18.168
r_dihedral_angle_4_deg15.017
r_dihedral_angle_1_deg5.467
r_scangle_it2.065
r_scbond_it1.411
r_angle_refined_deg1.071
r_angle_other_deg0.809
r_mcangle_it0.77
r_mcbond_it0.55
r_nbd_refined0.219
r_symmetry_vdw_refined0.19
r_nbtor_refined0.186
r_nbd_other0.172
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_other0.127
r_metal_ion_refined0.112
r_nbtor_other0.082
r_mcbond_other0.077
r_chiral_restr0.058
r_symmetry_hbond_refined0.057
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_xyhbond_nbd_other0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
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 AtomsNumber
Protein Atoms7637
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling