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Crystal structure of the adenosine kinase from Mus musculus in complex with adenosine and adenosine-diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 40% PEG400
15% PEG1000
0.15M Sodium di-potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.01 34.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.264 α = 90 b = 73.559 β = 90 c = 84.33 γ = 90
Symmetry Space Group P 21 21 21
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 2013-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 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 1.8 50 97.6 0.093 9.4 4.2 28540
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 1.8 1.83 98.8 0.732 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BX4 1.8 24.63 27048 1450 97.51 0.1673 0.1655 0.176 0.1999 0.2098 RANDOM 24.216
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 -0.19 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.768 r_dihedral_angle_4_deg 16.545 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 5.705 r_angle_refined_deg 1.849 r_mcangle_it 1.098 r_angle_other_deg 1.053 r_mcbond_it 0.686 r_mcbond_other 0.686 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.768 r_dihedral_angle_4_deg 16.545 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 5.705 r_angle_refined_deg 1.849 r_mcangle_it 1.098 r_angle_other_deg 1.053 r_mcbond_it 0.686 r_mcbond_other 0.686 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2679 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALEPACK data scaling HKL-2000 data reduction MOLREP phasing