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Crystal structure of the C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 (apo)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.473 α = 90 b = 194.857 β = 112.16 c = 84.441 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 100 PIXEL DECTRIS PILATUS 2M-F 2019-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999993 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 3.05 48.71 99.7 0.153 1 10.1 7 48030 -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 3.05 3.23 99.8 1.714 0.482 7.2
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 AB INITIO PHASING FREE R-VALUE 3.2 48.71 1.34 41655 1981 99.98 0.2249 0.2183 0.2265 0.276 0.2821
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 10.175 f_angle_d 0.483 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15712 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing