☰ Navigation Tabs
Bombyx mori GH32 beta-fructofuranosidase BmSUC1 mutant D63A in complex with sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 13% PEG 3350, 40 mM citric acid, 60 mM Bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.522 α = 90 b = 118.459 β = 90 c = 101.285 γ = 90
Symmetry Space Group C 2 2 21
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 S 6M 2019-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 50 99.9 0.063 13.1 6.4 42574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 0.661 2.1
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 1UYP 1.95 41.975 40878 2032 95.98 0.217 0.2159 0.226 0.2469 0.2556 50.272
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] 5.133 -3.174 -1.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.837 r_dihedral_angle_3_deg 13.509 r_dihedral_angle_4_deg 12.103 r_dihedral_angle_1_deg 8.424 r_lrange_it 3.689 r_lrange_other 3.637 r_scangle_it 1.826 r_scangle_other 1.826 r_mcangle_it 1.784 r_mcangle_other 1.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.837 r_dihedral_angle_3_deg 13.509 r_dihedral_angle_4_deg 12.103 r_dihedral_angle_1_deg 8.424 r_lrange_it 3.689 r_lrange_other 3.637 r_scangle_it 1.826 r_scangle_other 1.826 r_mcangle_it 1.784 r_mcangle_other 1.784 r_angle_refined_deg 1.318 r_angle_other_deg 1.149 r_scbond_it 1.123 r_scbond_other 1.123 r_mcbond_it 1.085 r_mcbond_other 1.085 r_nbd_other 0.186 r_nbd_refined 0.179 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3774 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing