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Crystal structure of the engineered C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 in complex with 1,5-InsP8 (phosphatase dead mutant, loop deletion residues 848-918)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 Morpheus II screen condition H2, 32.5% v/v Precipitant Mix 6: 25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol; 0.04M Polyamines: 0.01M Spermine tetrahydrochloride, 0.01M Spermidine trihydrochloride, 0.01M 1,4-Diaminobutane dihydrochloride, 0.01M DL-Ornithine monohydrochloride; 0.1M Buffer System 4: pH6.5 MOPSO, Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.586 α = 90 b = 114.586 β = 90 c = 172.179 γ = 120
Symmetry Space Group P 31 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 PILATUS 2M-F 2022-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.36 49.68 99.9 0.11 1 19.6 20.4 54137 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.51 99.6 2.95 0.52 1
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.36 49.68 1.35 54125 2707 99.91 0.2302 0.2279 0.2281 0.2746 0.2746
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 17.967 f_angle_d 0.572 f_chiral_restr 0.04 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7874 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 142
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing