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Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291.15 AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl.
Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant buffer containing 30% PEG 4000, 0.2 M NH4CH3CO2 (Ammonium Acetate), buffered with 100 mM CH3COONa (Sodium Acetate) adjusted to pH 4.6.
Crystal Properties Matthews coefficient Solvent content 2.47 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.754 α = 90 b = 82.226 β = 90 c = 78.783 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS 6M 2015-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97498 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 1.36 44.81 98.1 0.062 0.067 0.025 0.999 14.7 7.3 99761 16.56
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 1.36 1.41 96 1.017 1.094 0.397 0.682 1.9 7.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1AKE 1.36 44.81 1.33 99721 5028 97.82 0.1854 0.1843 0.1844 0.206 0.2058 21.65
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 18.8035 f_angle_d 1.5641 f_chiral_restr 0.1007 f_bond_d 0.0137 f_plane_restr 0.0119
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3312 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction