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The de novo designed hybrid alpha/beta-miniprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other not deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.2 M magnesium chloride hexahydrate
0.1 M HEPES pH 7.5
25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.937 α = 114.16 b = 32.068 β = 91.88 c = 43.087 γ = 109.86
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 PILATUS 6M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.1 50 87.3 0.027 0.99 24.5 3.5 49390 15.1
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 1.1 1.17 80.1 0.14 0.98 7.34 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT not deposited 1.1 29.02 48389 998 87.47 0.1299 0.1293 0.1402 0.1607 0.1726 RANDOM 14.162
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] -0.32 0.69 -0.63 0.37 -0.82 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.246 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_3_deg 11.278 r_rigid_bond_restr 10.584 r_dihedral_angle_1_deg 5.807 r_angle_refined_deg 2.762 r_angle_other_deg 1.643 r_chiral_restr 0.152 r_bond_refined_d 0.024 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.246 r_dihedral_angle_4_deg 18.512 r_dihedral_angle_3_deg 11.278 r_rigid_bond_restr 10.584 r_dihedral_angle_1_deg 5.807 r_angle_refined_deg 2.762 r_angle_other_deg 1.643 r_chiral_restr 0.152 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1110 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 19
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction