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Structure of Polyphosphate kinase 2 from Deinococcus radiodurans, in complex with ATP and polyphosphates.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 296.15 0.04 M potassium phosphate, 2% PEG 8000, 8% glycerol
Crystal Properties Matthews coefficient Solvent content 3.06 59.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.851 α = 90 b = 137.144 β = 116.895 c = 85.024 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 X 2M 2020-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.64 93.7 91.7 0.987 7.1 5.6 757195 16.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.781 0.655
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 7BMM 1.64 40.04 1.34 136223 6816 75.69 0.1703 0.1687 0.1662 0.2016 0.198 21.72
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 14.544 f_angle_d 1.1796 f_chiral_restr 0.0692 f_plane_restr 0.0138 f_bond_d 0.0124
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8632 Nucleic Acid Atoms Solvent Atoms 1256 Heterogen Atoms 439
Software Software Software Name Purpose autoPROC data processing PHENIX refinement autoPROC data reduction STARANISO data scaling PHASER phasing