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Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) from Cryptococcus neoformans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 0.1 M MES pH 6.0, 2.2 M ammonium sulfate, 50 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.9 57.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.81 α = 90 b = 59.74 β = 96.36 c = 379.674 γ = 90
Symmetry Space Group I 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 CCD ADSC QUANTUM 270 2015-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97929 PAL/PLS 7A (6B, 6C1)
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 2.35 50.61 98.9 0.135 0.159 0.082 0.985 5.7 3.6 88651 37.79
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 2.35 2.39 99 0.624 0.733 0.377 0.501 3.7 4592
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.35 37.37 1.35 88613 4401 98.79 0.2358 0.2342 0.2376 0.267 0.2686 52.2376
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 13.886 f_angle_d 1.059 f_chiral_restr 0.045 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11380 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement Aimless data scaling SOLVE phasing PDB_EXTRACT data extraction iMOSFLM data reduction