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Crystal structure of a GH31 family sulfoquinovosidase mutant D455N from Agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (SQGro)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 24% PEG 3350 w/v, 0.2 M KSCN, 0.1 M Bis-Tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.534 α = 90 b = 168.396 β = 116.53 c = 100.687 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 EIGER2 XE 16M 2019-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.15 61.51 97.4 0.09 0.109 0.061 0.993 8.1 2.9 153301
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 98.9 0.686 0.829 0.459 0.624 2.9
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 5OHT 2.15 61.01 145522 7734 97.36 0.1957 0.1942 0.1986 0.2236 0.2257 RANDOM 28.618
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] 0.58 -1.76 -0.38 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.461 r_dihedral_angle_4_deg 17.651 r_dihedral_angle_3_deg 13.885 r_dihedral_angle_1_deg 7.215 r_angle_refined_deg 1.502 r_angle_other_deg 1.347 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.461 r_dihedral_angle_4_deg 17.651 r_dihedral_angle_3_deg 13.885 r_dihedral_angle_1_deg 7.215 r_angle_refined_deg 1.502 r_angle_other_deg 1.347 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20405 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 80
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing