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A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ
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
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.2 α = 90 b = 169.19 β = 92.8 c = 169.69 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 1.97 75.77 99.8 0.0779 0.998 11.6 4.1 411803
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 1.97 2.02 100 0.965 0.558 1.4 4.2
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 1.97 75.77 411803 20006 99.75 0.182 0.181 0.1876 0.2026 0.2087 RANDOM 34.7035
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] -0.12 0.19 -1.03 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 14.038 r_dihedral_angle_1_deg 6.399 r_angle_other_deg 3.798 r_angle_refined_deg 1.871 r_mcangle_it 1.629 r_mcbond_it 1.043 r_mcbond_other 1.038 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 14.038 r_dihedral_angle_1_deg 6.399 r_angle_other_deg 3.798 r_angle_refined_deg 1.871 r_mcangle_it 1.629 r_mcbond_it 1.043 r_mcbond_other 1.038 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_other 0.017 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41583 Nucleic Acid Atoms Solvent Atoms 2168 Heterogen Atoms 368
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling Coot model building MOLREP phasing