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Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with neo-IP5 and ATP
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 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.632 α = 87.81 b = 60.563 β = 88.43 c = 84.482 γ = 63.01
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 2012-01-31 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 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 2.65 29.34 90.8 0.127 0.169 0.11 0.98 3.5 2.1 27766 47.33
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 2.65 2.78 89.9 0.705 0.945 0.625 0.348 2.1
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 THROUGHOUT 2XAM 2.65 29.335 1.96 27753 1425 90.82 0.2031 0.1993 0.2017 0.2681 0.2698 52.4975
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 17.794 f_angle_d 1.176 f_chiral_restr 0.05 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6616 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 242
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction