3C4Z

Crystal structure of G protein coupled receptor kinase 1 bound to ADP and magnesium chloride at 1.84A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C4WPDB ENTRY 3C4W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.25293PEG 6000, NaCl, glycerol, MES pH 6.25, ADP, magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3748.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.54α = 90
b = 82.947β = 93.01
c = 107.144γ = 90
Symmetry
Space GroupC 1 2 1

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
11.843049154

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 3C4W1.8419.474933899.350.192750.1927530.417
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]
-0.23-0.130.49-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.674
r_dihedral_angle_3_deg13.59
r_dihedral_angle_4_deg12.681
r_dihedral_angle_1_deg5.368
r_scangle_it4.32
r_scbond_it3.261
r_mcangle_it1.7
r_mcbond_it1.368
r_angle_refined_deg1.175
r_angle_other_deg0.837
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.674
r_dihedral_angle_3_deg13.59
r_dihedral_angle_4_deg12.681
r_dihedral_angle_1_deg5.368
r_scangle_it4.32
r_scbond_it3.261
r_mcangle_it1.7
r_mcbond_it1.368
r_angle_refined_deg1.175
r_angle_other_deg0.837
r_nbd_refined0.204
r_symmetry_vdw_other0.187
r_nbtor_refined0.18
r_nbd_other0.179
r_mcbond_other0.173
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.154
r_symmetry_vdw_refined0.119
r_nbtor_other0.083
r_chiral_restr0.065
r_metal_ion_refined0.034
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms3962
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms31

Software

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