2QRE

Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide (ZMP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OOY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52936-10% PEG 3350, 0.1M sodium citrate, pH 5.5, 2mM ZMP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.47α = 90
b = 78.146β = 124.04
c = 108.512γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97926APS24-ID-C

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
135089.30.184.63.9217902082611
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)
133.11960.631.53.32232

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT200y3.0141.34112059019774104889.150.3030.238530.23540.29736RANDOM89.957
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]
-0.47-1.53-0.62-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.578
r_dihedral_angle_3_deg21.108
r_dihedral_angle_4_deg18.907
r_dihedral_angle_1_deg6.465
r_scangle_it1.466
r_angle_refined_deg1.439
r_scbond_it0.889
r_mcangle_it0.657
r_mcbond_it0.366
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.578
r_dihedral_angle_3_deg21.108
r_dihedral_angle_4_deg18.907
r_dihedral_angle_1_deg6.465
r_scangle_it1.466
r_angle_refined_deg1.439
r_scbond_it0.889
r_mcangle_it0.657
r_mcbond_it0.366
r_nbtor_refined0.311
r_nbd_refined0.229
r_symmetry_vdw_refined0.21
r_xyhbond_nbd_refined0.18
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8130
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing