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Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with myo-IP6 and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 18 % PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2, 25% EG or 35% PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.81 α = 88.53 b = 60.34 β = 89.18 c = 83.98 γ = 63.36
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-F 2011-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.025 83.952 89.6 0.068 0.099 0.07 6.9 1.9 61224 28.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.025 2.08 89.9 0.219 0.219 0.584 0.413 3.5 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 THROUGHOUT 2XAM 2.025 83.952 1.97 61203 3100 89.54 0.1803 0.1779 0.1807 0.2254 0.224 RANDOM SELECTION 40.5667
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 12.666 f_angle_d 0.961 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6675 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 187
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing