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Crystal structure of sulfoquinovose dioxygenase from Marinobacterium aestuarii in complex with Mn(II) and succinate
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 2.61 52.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.639 α = 90 b = 117.648 β = 90 c = 59.07 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 2024-07-05 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 1.57 47.48 99.5 1 11.1 6.5 52605
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 1.57 1.6 0.84
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 1.573 39.939 52587 2604 99.468 0.167 0.166 0.1792 0.1891 0.201 15.005
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] 1.065 -0.136 -0.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.441 r_dihedral_angle_3_deg 12.339 r_dihedral_angle_2_deg 9.173 r_dihedral_angle_1_deg 6.5 r_lrange_it 4.96 r_lrange_other 4.614 r_scangle_it 3.274 r_scangle_other 3.26 r_scbond_it 2.055 r_scbond_other 2.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.441 r_dihedral_angle_3_deg 12.339 r_dihedral_angle_2_deg 9.173 r_dihedral_angle_1_deg 6.5 r_lrange_it 4.96 r_lrange_other 4.614 r_scangle_it 3.274 r_scangle_other 3.26 r_scbond_it 2.055 r_scbond_other 2.043 r_mcangle_it 1.864 r_mcangle_other 1.864 r_angle_refined_deg 1.473 r_mcbond_it 1.189 r_mcbond_other 1.189 r_angle_other_deg 0.538 r_nbd_refined 0.207 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.18 r_nbd_other 0.176 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbd_refined 0.082 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.076 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing