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De novo design protein -N9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other design model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 20% w/v PEG 10000 0.1M Hepes ph7.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.011 α = 90 b = 75.997 β = 90 c = 129.64 γ = 90
Symmetry Space Group C 2 2 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 6M 2023-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.35 43.21 100 1 21.2 9 38537 15.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 0.817
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 1.35 25.61 1.34 38477 1939 99.96 0.2031 0.2018 0.2028 0.2273 0.2288 21.31
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 11.1993 f_angle_d 0.8422 f_chiral_restr 0.0739 f_plane_restr 0.0096 f_bond_d 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1432 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing