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Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate
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 10% PEG 3350, 0.2 M magnesium acetate, 10 mM alpha-glucopyranosyl fluoride
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.36 α = 90 b = 128.3 β = 90 c = 154.42 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 2M 2019-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.7 50 99.5 0.127 0.989 7.9 4.7 140237
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 1.7 1.79 99.1 0.683 0.672 2 4.3
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 1.7 49.49 133124 6972 99.36 0.1845 0.1831 0.1931 0.2112 0.2201 RANDOM 24.814
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] 0.3 0.14 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.385 r_dihedral_angle_4_deg 15.244 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_1_deg 7.119 r_angle_refined_deg 1.345 r_angle_other_deg 1.34 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.385 r_dihedral_angle_4_deg 15.244 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_1_deg 7.119 r_angle_refined_deg 1.345 r_angle_other_deg 1.34 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9251 Nucleic Acid Atoms Solvent Atoms 822 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing