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A GH31 family sulfoquinovosidase in complex with aza-sugar inhibitor IFGSQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein stock at 45 mg/mL in the buffer of 50 mM NaPO4 and 500 mM NaCl is mixed with the precipitant of 0.2 M KSCN, 21% PEG3350, 0.1 M bis-Tris propane pH 6.5, at a ratio of 1.2: 1.
Crystal Properties Matthews coefficient Solvent content 2.5 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.29 α = 90 b = 168.82 β = 117.07 c = 101.39 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M-F 2016-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
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 1.77 77.8 99.9 0.0817 0.996 11.9 4.2 284814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.82 99.9 0.534 1.1 4.1
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 apo 1.77 77.7 284768 14049 99.82 0.1777 0.1768 0.1835 0.1954 0.2009 RANDOM 33.9606
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] 0.96 -0.72 0.09 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.706 r_dihedral_angle_4_deg 15.999 r_dihedral_angle_3_deg 13.034 r_dihedral_angle_1_deg 6.356 r_angle_other_deg 3.789 r_mcangle_it 2.083 r_angle_refined_deg 1.657 r_mcbond_it 1.511 r_mcbond_other 1.478 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.706 r_dihedral_angle_4_deg 15.999 r_dihedral_angle_3_deg 13.034 r_dihedral_angle_1_deg 6.356 r_angle_other_deg 3.789 r_mcangle_it 2.083 r_angle_refined_deg 1.657 r_mcbond_it 1.511 r_mcbond_other 1.478 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_other 0.013 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20697 Nucleic Acid Atoms Solvent Atoms 1818 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing