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A GH31 family sulfoquinovosidase from E. coli in complex with aza-sugar inhibitor IFGSQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25 MG/ML-1 PROTEIN IN 50 MM NAPO4 , PH6.5, AND 250 MM NACL BUFFER IS MIXED WITH EQUAL VOLUME OF PRECIPITANT COMPOSED OF 50-60% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1-0.15 M CACL2, AND 20 DEGREE
Crystal Properties Matthews coefficient Solvent content 2.9 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.473 α = 100.76 b = 86.269 β = 113.77 c = 86.81 γ = 97.14
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 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.87 44.62 97.8 0.0378 0.999 14.8 3.5 140829
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 1.87 1.9 96.9 0.797 0.622 1.2 3.6
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 5aee 1.87 44.62 140828 6991 97.76 0.1678 0.166 0.1764 0.2018 0.2114 RANDOM 42.6633
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] 0.07 -1.59 0.16 -2.68 -0.14 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 15.955 r_dihedral_angle_3_deg 13.399 r_dihedral_angle_1_deg 6.92 r_mcangle_it 4.621 r_angle_other_deg 3.875 r_mcbond_it 3.719 r_mcbond_other 3.719 r_angle_refined_deg 1.702 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 15.955 r_dihedral_angle_3_deg 13.399 r_dihedral_angle_1_deg 6.92 r_mcangle_it 4.621 r_angle_other_deg 3.875 r_mcbond_it 3.719 r_mcbond_other 3.719 r_angle_refined_deg 1.702 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10675 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling MOLREP phasing