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An enumerative algorithm for de novo design of proteins with diverse pocket structures
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Design Model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.09 M Sodium nitrate, 0.09 Sodium phosphate dibasic, 0.09 M Ammonium sulfate; 0.1 M Tris (base) & BICINE pH 8.5; 12.5 % v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.864 α = 90 b = 48.864 β = 90 c = 84.576 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC QUANTUM 315r 2019-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.55 42.31 100 0.115 0.032 0.999 13.7 13.7 15581 22.08
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 1.55 1.58 0.423 0.8
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 Design Model 1.55 42.31 1.43 15519 1553 99.94 0.1985 0.1951 0.196 0.2279 0.2285 29.83
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 9.8641 f_angle_d 0.6329 f_chiral_restr 0.0484 f_bond_d 0.0038 f_plane_restr 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 896 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing