5KB5

Crystal structure of the adenosine kinase from Mus musculus in complex with adenosine and adenosine-diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BX4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529140% PEG400 15% PEG1000 0.15M Sodium di-potassium phosphate
Crystal Properties
Matthews coefficientSolvent content
2.0134.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.264α = 90
b = 73.559β = 90
c = 84.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.459LNLSW01B-MX2

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
11.85097.60.0939.44.228540
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)
11.81.8398.80.7324.2

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 REPLACEMENTTHROUGHOUT1BX41.824.6327048145097.510.16730.16550.1999RANDOM24.216
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]
-0.1-0.190.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.768
r_dihedral_angle_4_deg16.545
r_dihedral_angle_3_deg14.661
r_dihedral_angle_1_deg5.705
r_angle_refined_deg1.849
r_mcangle_it1.098
r_angle_other_deg1.053
r_mcbond_it0.686
r_mcbond_other0.686
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.768
r_dihedral_angle_4_deg16.545
r_dihedral_angle_3_deg14.661
r_dihedral_angle_1_deg5.705
r_angle_refined_deg1.849
r_mcangle_it1.098
r_angle_other_deg1.053
r_mcbond_it0.686
r_mcbond_other0.686
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2679
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms86

Software

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