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Crystal structure of sulfoquinovose dioxygenase from Marinobacterium aestuarii in complex with sulfoquinovose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.6 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.732 α = 90 b = 118.252 β = 90 c = 59.053 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2024-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.45 47.48 99.9 1 15 6.8 71275
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 1.45 1.47 0.81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 47.48 66974 3379 99.846 0.128 0.1263 0.1262 0.1603 0.1602 18.129
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] 1.164 -0.393 -0.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.003 r_lrange_it 15.928 r_lrange_other 13.744 r_dihedral_angle_3_deg 12.003 r_scangle_it 8.959 r_scangle_other 8.787 r_dihedral_angle_2_deg 8.655 r_mcangle_it 6.603 r_mcangle_other 6.603 r_dihedral_angle_1_deg 6.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.003 r_lrange_it 15.928 r_lrange_other 13.744 r_dihedral_angle_3_deg 12.003 r_scangle_it 8.959 r_scangle_other 8.787 r_dihedral_angle_2_deg 8.655 r_mcangle_it 6.603 r_mcangle_other 6.603 r_dihedral_angle_1_deg 6.247 r_scbond_it 6.023 r_scbond_other 5.882 r_mcbond_it 4.293 r_mcbond_other 4.288 r_rigid_bond_restr 2.908 r_angle_refined_deg 1.593 r_angle_other_deg 0.594 r_nbd_other 0.263 r_nbd_refined 0.233 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.177 r_xyhbond_nbd_other 0.131 r_symmetry_nbd_refined 0.129 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.038 r_gen_planes_refined 0.008 r_bond_refined_d 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 2534 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing