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Crystal structure of silkworm fibroinase complexed with E-64
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 30% w/v Polyethylene glycol monomethyl ether 2,000, 0.1 M Potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.19 43.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.18 α = 90 b = 64.69 β = 97.641 c = 92.91 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 PILATUS3 6M 2019-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.56 92.09 99.6 0.131 0.143 0.055 8.1 6.7 58638
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.6 98.8 0.392 0.425 0.164 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.56 92.085 58624 2863 99.58 0.233 0.2313 0.2329 0.2693 0.2698 15.376
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] -1.645 0.077 -0.904 2.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.002 r_dihedral_angle_4_deg 15.972 r_dihedral_angle_3_deg 13.245 r_dihedral_angle_1_deg 7.227 r_lrange_it 3.741 r_lrange_other 3.722 r_scangle_it 2.953 r_scangle_other 2.952 r_scbond_it 1.935 r_scbond_other 1.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.002 r_dihedral_angle_4_deg 15.972 r_dihedral_angle_3_deg 13.245 r_dihedral_angle_1_deg 7.227 r_lrange_it 3.741 r_lrange_other 3.722 r_scangle_it 2.953 r_scangle_other 2.952 r_scbond_it 1.935 r_scbond_other 1.935 r_mcangle_other 1.869 r_mcangle_it 1.868 r_angle_refined_deg 1.601 r_angle_other_deg 1.441 r_mcbond_it 1.212 r_mcbond_other 1.204 r_nbd_refined 0.216 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.171 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.142 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3360 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing