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Bombyx mori GH13 sucrose hydrolase complexed with 1,4-dideoxy-1,4-imino-D-arabinitol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 8% PEG 3350, 0.2 M magnesium acetate, 10 mM 1,4-dideoxy-1,4-imino-D-arabinitol
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.054 α = 90 b = 146.444 β = 90 c = 153.291 γ = 90
Symmetry Space Group P 21 21 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 1.0 Photon Factory BL-5A
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 1.75 50 100 0.074 0.999 15.4 6.6 148203
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 1.75 1.84 100 0.889 0.755 2.2 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5BRQ 1.75 48.29 140585 7335 99.95 0.1632 0.1621 0.1837 0.1799 RANDOM 28.54
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] 0.48 -1.56 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.81 r_dihedral_angle_4_deg 15.65 r_dihedral_angle_3_deg 12.617 r_dihedral_angle_1_deg 6.956 r_angle_other_deg 1.314 r_angle_refined_deg 1.301 r_chiral_restr 0.063 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.81 r_dihedral_angle_4_deg 15.65 r_dihedral_angle_3_deg 12.617 r_dihedral_angle_1_deg 6.956 r_angle_other_deg 1.314 r_angle_refined_deg 1.301 r_chiral_restr 0.063 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9302 Nucleic Acid Atoms Solvent Atoms 1021 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PDB_EXTRACT data extraction MOLREP phasing