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De novo designed N37 protein fold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 0.2 M Potassium thiocyanate 0.1 M Sodium acetate 5.5 25 % w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.76 α = 78.814 b = 66.84 β = 74.747 c = 81.12 γ = 62.558
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 EIGER X 4M 2024-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.87313 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 2.199 77.98 98 0.137 0.995 7.3 4 56016 32.53
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 2.199 2.237 97.2 1.042 0.551 1.3 4.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 77.98 1.97 55975 2831 97.95 0.2009 0.1991 0.2318 0.2191 44.31
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 11.3972 f_angle_d 0.3873 f_chiral_restr 0.0375 f_plane_restr 0.0025 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8959 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction XSCALE data scaling PHASER phasing