2Y8L

Structure of the regulatory fragment of mammalian aMPK in complex with two ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V8QPDB ENTRY 2V8Q

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.2862.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.567α = 90
b = 121.464β = 90
c = 125.922γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
12.520980.0623.15.924672
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)
12.52.5985.80.313.55.1

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 ENTRY 2V8Q2.587.4224672131497.80.2290.2280.253RANDOM60.25
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]
-2.392.95-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.357
r_dihedral_angle_4_deg20.021
r_dihedral_angle_3_deg19.564
r_dihedral_angle_1_deg6.712
r_scangle_it2.158
r_angle_refined_deg1.428
r_scbond_it1.296
r_mcangle_it1.048
r_mcbond_it0.555
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.357
r_dihedral_angle_4_deg20.021
r_dihedral_angle_3_deg19.564
r_dihedral_angle_1_deg6.712
r_scangle_it2.158
r_angle_refined_deg1.428
r_scbond_it1.296
r_mcangle_it1.048
r_mcbond_it0.555
r_chiral_restr0.103
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3867
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing