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Domain swapped dimer of smolstatin (stefin) from Sphaerospora molnari
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.1 M calcium chloride dihydrate, 20% w/v PEG 6000, 10% v/v ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.48 50.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.508 α = 90 b = 97.867 β = 101.914 c = 38.626 γ = 90
Symmetry Space Group P 1 21 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 2021-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.99 37.79 98.48 0.07964 0.997 13.6 6.8 14976
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 1.991 2.062 0.933
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 1.991 37.79 14975 749 98.507 0.201 0.1987 0.2016 0.2452 0.2509 41.327
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] 2.993 2.911 -4.583 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.428 r_dihedral_angle_4_deg 23.816 r_dihedral_angle_3_deg 15.524 r_lrange_other 7.154 r_lrange_it 7.142 r_dihedral_angle_1_deg 6.682 r_scangle_it 5.716 r_scangle_other 5.714 r_mcangle_it 4.619 r_mcangle_other 4.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.428 r_dihedral_angle_4_deg 23.816 r_dihedral_angle_3_deg 15.524 r_lrange_other 7.154 r_lrange_it 7.142 r_dihedral_angle_1_deg 6.682 r_scangle_it 5.716 r_scangle_other 5.714 r_mcangle_it 4.619 r_mcangle_other 4.617 r_scbond_it 3.976 r_scbond_other 3.973 r_mcbond_it 3.363 r_mcbond_other 3.353 r_angle_other_deg 1.442 r_angle_refined_deg 1.32 r_xyhbond_nbd_refined 0.266 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.217 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_other 0.175 r_nbd_other 0.12 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1451 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 16
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing