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Crystal structure of sulfoquinovose-1-dehydrogenase from Pseudomonas Putida (sulfo-ED pathway)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P0DOV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 apo-SQDH was grown using a 20 mg/mL protein solution in 50 mM TRIS buffer pH 7.5 containing 300 mM NaCl in a drop with 0.15 uL protein: 0.15 uL mother liquor, the latter comprising 0.1 M MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid) buffer pH 7.0 and 25% w/v PEG (polyethylene glycol) 1500.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.727 α = 90 b = 57.293 β = 93.4 c = 91.267 γ = 90
Symmetry Space Group I 1 2 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 X 16M 2023-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.7 63.07 99.3 0.079 0.086 0.033 0.997 12.8 6.7 46667
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 1.7 1.73 99.8 0.883 0.956 0.362 0.761 6.8
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 (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 1.7 63.07 44228 2394 99.15 0.19677 0.1946 0.1946 0.23706 0.237 RANDOM 32.591
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] -1.48 0.07 1.57 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.435 r_dihedral_angle_2_deg 10.586 r_dihedral_angle_1_deg 6.367 r_long_range_B_refined 6.022 r_scbond_it 3.632 r_mcangle_it 2.944 r_angle_refined_deg 2.468 r_mcbond_it 2.229 r_chiral_restr 0.166 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.435 r_dihedral_angle_2_deg 10.586 r_dihedral_angle_1_deg 6.367 r_long_range_B_refined 6.022 r_scbond_it 3.632 r_mcangle_it 2.944 r_angle_refined_deg 2.468 r_mcbond_it 2.229 r_chiral_restr 0.166 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3793 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction BALBES phasing