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Computationally Designed Thioredoxin dF106
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FB0 1FB0 and 2PUK experimental model PDB 2PUK 1FB0 and 2PUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100-150mM lithium citrate, 100mM imidazole pH 7.0, 1mM (NH4)2SO4, 10%PEG4000, and 5mM CuCl2
Crystal Properties Matthews coefficient Solvent content 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.07 α = 90 b = 67.95 β = 90 c = 229.451 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 2M 2015-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 41.2 100 0.04211 0.995 11.47 2 36480
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 2.4 2.486 100 0.2978 2.68 2
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 1FB0 and 2PUK 2.4 41.2 1.35 36471 1824 99.96 0.2043 0.2007 0.2037 0.2734 0.2744
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 11.786 f_angle_d 0.999 f_chiral_restr 0.052 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6532 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing