☰ Navigation Tabs
Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0,04 M potassium phosphate
2% PEG 8K
8% glycerol
Crystal Properties Matthews coefficient Solvent content 3.01 59.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.925 α = 90 b = 78.605 β = 109.207 c = 111.451 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 80 PIXEL DECTRIS PILATUS3 6M 2020-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 2.06 83.98 92.5 0.987 6.3 6.9 46075 21.77
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 2.06 2.346 72.8 0.537 6.8
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 6aqe 2.06 83.98 1.34 46055 2146 51.26 0.1967 0.1942 0.1932 0.2462 0.2418 30.71
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 11.9233 f_angle_d 0.5007 f_chiral_restr 0.0393 f_plane_restr 0.0039 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8632 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 44
Software Software Software Name Purpose Coot model building PHENIX refinement PHASER phasing STARANISO data scaling XDS data reduction