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Crystal structure of the computationally designed Scone-R protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M magnesium acetate
0.1 M sodium acetate
4% (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.077 α = 90 b = 79.834 β = 100.984 c = 47.426 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 PILATUS3 6M 2018-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.5 46.56 99.8 0.037 0.042 0.019 0.999 16.8 4.5 46828 20.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.2 0.536 0.606 0.278 0.864 2.4 4.6
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 6TJG 1.5 46.56 0.61 46792 2322 99.79 0.164 0.1625 0.1636 0.1908 0.1924 25.22
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 18.9138 f_angle_d 1.2448 f_chiral_restr 0.0821 f_bond_d 0.0145 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2470 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing