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Structure of the T175V Etr1p mutant in the trigonal form P312 in complex with NADP and crotonyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 298 Etr1p was crystallized at 15 mg/mL with 5 mM NADP and 5 mM of crotonyl-CoA in the gel filtration buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.9). Crystals appeared after several days in 2.0 M (NH4)2SO4, 100 mM ADA/NaOH pH 6.4 at room temperature.
The crystals were soaked in a solution containing 30% (v/v) glycerol, 2.0 M (NH4)2SO4, 100 mM ADA pH 6.4 prior to freezing in liquid nitrogen to prevent water-crystal formation.
Crystal Properties Matthews coefficient Solvent content 3.47 64.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.498 α = 90 b = 93.498 β = 90 c = 231.203 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 6M-F 2015-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.73913 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.5 47.04 100 0.124 0.044 0.997 12.2 8.6 41476
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 1.511 1.5 7.7
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 FREE R-VALUE 4W99 2.5 46.749 1.33 41370 1958 99.84 0.1835 0.182 0.1854 0.2124 0.2153
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 15.216 f_angle_d 1.002 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5596 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 224
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing