☰ Navigation Tabs
The de novo designed hybrid alpha/beta-miniprotein (with Se-Methionine)
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 8.5 291 0.2 M magnesium chloride hexahydrate
0.1 M Tris pH 8.5
20 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.089 α = 90 b = 35.481 β = 111.24 c = 41.919 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2019-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 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 1.15 50 97.6 0.05 0.99 16.61 6.3 24712 18.1
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 1.15 1.22 88.5 0.43 0.91 2.95 5.6
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 1.15 39.07 23711 1001 97.79 0.1763 0.1745 0.1806 0.2202 0.2275 RANDOM 20.083
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] -0.09 0.32 -2.34 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.387 r_dihedral_angle_4_deg 22.652 r_dihedral_angle_3_deg 12.71 r_rigid_bond_restr 7.962 r_dihedral_angle_1_deg 5.819 r_angle_refined_deg 2.558 r_angle_other_deg 1.569 r_chiral_restr 0.148 r_bond_refined_d 0.02 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.387 r_dihedral_angle_4_deg 22.652 r_dihedral_angle_3_deg 12.71 r_rigid_bond_restr 7.962 r_dihedral_angle_1_deg 5.819 r_angle_refined_deg 2.558 r_angle_other_deg 1.569 r_chiral_restr 0.148 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 508 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 8
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction