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Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M magnesium chloride, 0.1 M Tris, pH 7.0, 10% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.917 α = 90 b = 89.917 β = 90 c = 124.897 γ = 120
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 EIGER2 X 16M 2021-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 3.25 48.99 100 0.119 0.998 10.2 8.6 5943 81.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.51 100 0.261 0.975 5.5 8.6
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 3.25 41.63 2.06 5938 292 99.97 0.2419 0.2398 0.2374 0.2849 0.2819 76.88
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 15.0836 f_angle_d 0.3356 f_chiral_restr 0.0296 f_plane_restr 0.0033 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2386 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing