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High-resolution structure of the adenosine kinase from Mus musculus in complex with adenosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 50% (v/v) PEG400
0.2 M lithium sulphate
0.1 M sodium acetate
2.5 mM adenosine
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.839 α = 90 b = 82.159 β = 92.69 c = 89.189 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2013-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 0.954 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.2 50 99.8 0.054 12 4 228026
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 99.9 0.653 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.2 20.76 216557 11429 99.72 0.1417 0.1408 0.1589 0.165 RANDOM 19.828
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] 0.22 -0.13 -0.1 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.583 r_sphericity_free 29.46 r_dihedral_angle_4_deg 14.657 r_dihedral_angle_3_deg 11.577 r_sphericity_bonded 11.226 r_dihedral_angle_1_deg 5.671 r_rigid_bond_restr 1.963 r_mcangle_it 1.514 r_angle_refined_deg 1.387 r_mcbond_it 1.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.583 r_sphericity_free 29.46 r_dihedral_angle_4_deg 14.657 r_dihedral_angle_3_deg 11.577 r_sphericity_bonded 11.226 r_dihedral_angle_1_deg 5.671 r_rigid_bond_restr 1.963 r_mcangle_it 1.514 r_angle_refined_deg 1.387 r_mcbond_it 1.099 r_mcbond_other 1.095 r_angle_other_deg 0.918 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5390 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing DENZO data reduction