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Bombyx mori GH13 sucrose hydrolase mutant E322Q complexed with sucrose
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 sucrose
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.7 α = 90 b = 127.9 β = 90 c = 154.3 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 2019-11-03 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 1.84 50 99.9 0.097 0.998 12.4 6.5 111648
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 1.84 1.94 100 0.775 0.769 2.4 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5BRQ 1.84 49.28 105891 5621 99.85 0.1823 0.1808 0.1891 0.2114 0.2182 RANDOM 26.004
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] 0.05 0.07 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.136 r_dihedral_angle_4_deg 16.607 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 7.246 r_angle_other_deg 2.356 r_angle_refined_deg 1.6 r_chiral_restr 0.079 r_bond_other_d 0.036 r_gen_planes_other 0.013 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.136 r_dihedral_angle_4_deg 16.607 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 7.246 r_angle_other_deg 2.356 r_angle_refined_deg 1.6 r_chiral_restr 0.079 r_bond_other_d 0.036 r_gen_planes_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9251 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing