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Molecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AKE 4AKE_A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 32% PEG 8000, 0.2 M Na-Acetate, 0.1 M Na-Cacodylate
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.88 α = 90 b = 31.779 β = 112.35 c = 54.205 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 6M 2016-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97939 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.4 33.1 96.3 0.052 0.059 0.036 0.998 11.2 4.4 89469 12.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.47 92.2 0.99 1.13 0.63 0.71 1.42 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4AKE_A 1.4 33.1 1.35 41048 915 98.32 0.1754 0.175 0.1776 0.1903 0.1936 Random selection 29
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.054 f_angle_d 1.083 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing