3NYN

Crystal Structure of G Protein-Coupled Receptor Kinase 6 in Complex with Sangivamycin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.227710 mg/ml GRK6 mixed 1:1 with well containing 1.9 M AMS and 100 mM Bis-Tris, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
5.6278.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.59α = 90
b = 154.59β = 90
c = 207.914γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 300 mm CCD2008-08-11SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.74059.40.0888.13.97702145850-2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.751.20.3514.8

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.72304346645750228460.430.227090.227090.2384RANDOM99.517
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]
4.752.384.75-7.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.219
r_dihedral_angle_4_deg15.431
r_dihedral_angle_3_deg15.162
r_dihedral_angle_1_deg5.13
r_mcangle_it1.639
r_scangle_it1.365
r_angle_refined_deg1.064
r_mcbond_it0.9
r_scbond_it0.765
r_angle_other_deg0.754
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.219
r_dihedral_angle_4_deg15.431
r_dihedral_angle_3_deg15.162
r_dihedral_angle_1_deg5.13
r_mcangle_it1.639
r_scangle_it1.365
r_angle_refined_deg1.064
r_mcbond_it0.9
r_scbond_it0.765
r_angle_other_deg0.754
r_mcbond_other0.068
r_chiral_restr0.054
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_refined0.001
r_gen_planes_other
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 AtomsNumber
Protein Atoms8908
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms126

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction