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Bombyx mori GH32 beta-fructofuranosidase BmSUC1
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 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.752 α = 90 b = 119.308 β = 90 c = 100.275 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 2020-03-06 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 1.8 50 99.9 0.051 17 6 52834
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 1.8 1.9 0.607 2.5
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 (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 1.8 42.872 52623 2559 99.518 0.17 0.1678 0.1798 0.2131 0.2236 39.454
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] 4.91 -1.012 -3.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.94 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_4_deg 12.985 r_dihedral_angle_1_deg 8.546 r_lrange_it 2.876 r_lrange_other 2.869 r_scangle_it 2.411 r_scangle_other 2.411 r_mcangle_it 2.192 r_mcangle_other 2.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.94 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_4_deg 12.985 r_dihedral_angle_1_deg 8.546 r_lrange_it 2.876 r_lrange_other 2.869 r_scangle_it 2.411 r_scangle_other 2.411 r_mcangle_it 2.192 r_mcangle_other 2.192 r_rigid_bond_restr 2.096 r_scbond_it 1.922 r_scbond_other 1.922 r_mcbond_it 1.71 r_mcbond_other 1.71 r_angle_refined_deg 1.523 r_angle_other_deg 1.292 r_symmetry_xyhbond_nbd_refined 0.274 r_nbd_other 0.227 r_nbd_refined 0.191 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.119 r_symmetry_nbd_refined 0.081 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3777 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MrBUMP phasing