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Bombyx mori GH13 sucrose hydrolase complexed with acarbose
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, 2 mM acarbose
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.247 α = 90 b = 145.792 β = 90 c = 152.857 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 1.75 50 100 0.08 0.999 18.7 12.3 147455
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 0.805 0.846 2.8 11.9
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 1.75 48.66 139957 7296 99.92 0.1988 0.1973 0.2092 0.2285 0.2377 RANDOM 29.698
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] -0.03 0.24 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.884 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 13.598 r_dihedral_angle_1_deg 7.391 r_angle_refined_deg 1.689 r_angle_other_deg 1.414 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.884 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 13.598 r_dihedral_angle_1_deg 7.391 r_angle_refined_deg 1.689 r_angle_other_deg 1.414 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9295 Nucleic Acid Atoms Solvent Atoms 610 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing