2OOY

Crystal structure of the adenylate sensor from AMP-activated protein kinase complexed with ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OOXPDB entry 2OOX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52937.3-8.1% PEG3350, 0.1M HEPES, pH 7.5, 5mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.902α = 90
b = 77.666β = 123.99
c = 107.576γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97898NSLSX4A

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
12.885096.20.18.32.725963249692
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)
2.88393.40.417

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB entry 2OOX2.885012496923704126596.280.19460.189020.29784RANDOM54.539
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]
-0.260.361.21-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.181
r_dihedral_angle_4_deg24.444
r_dihedral_angle_3_deg23.74
r_dihedral_angle_1_deg9.963
r_scangle_it3.802
r_angle_refined_deg2.37
r_scbond_it2.313
r_mcangle_it1.909
r_mcbond_it1.075
r_symmetry_vdw_refined0.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.181
r_dihedral_angle_4_deg24.444
r_dihedral_angle_3_deg23.74
r_dihedral_angle_1_deg9.963
r_scangle_it3.802
r_angle_refined_deg2.37
r_scbond_it2.313
r_mcangle_it1.909
r_mcbond_it1.075
r_symmetry_vdw_refined0.381
r_nbtor_refined0.35
r_nbd_refined0.333
r_xyhbond_nbd_refined0.304
r_symmetry_hbond_refined0.249
r_chiral_restr0.154
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8507
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing