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The DYW domain of A. thaliana OTP86 in its active state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O4E D_1292114961
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 100 nl protein plus 100 nl reservoir (0.1 M glycine, pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4) plus 30 nl additive (0.1 M 50% v/v Jeffamine M-600 pH 7.0). Cryo: reservoir solution supplemented with 15% (v/v) ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 1.97 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.599 α = 90 b = 132.883 β = 90 c = 30.633 γ = 90
Symmetry Space Group P 21 21 2
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 2020-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.65 44.03 97.7 0.151 0.157 1 10.3 12.7 57997 18.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 94.9 1.724 1.802 0.764 1.31 11.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292114961 1.65 44.03 1.34 57767 2095 97.31 0.2226 0.2208 0.2677 0.2319 38.54
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 25.7597 f_angle_d 1.2124 f_chiral_restr 0.0709 f_bond_d 0.012 f_plane_restr 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4428 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 8
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement