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Crystal structure of the persulfide dioxygenase (PDO - PA2915) from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 1.5 microL of protein solution (8 mg/mL) with 1 microL of the reservoir solution (Morpheus Molecular dimension A9) containing: 0.06 M Divalents (0.03 M Magnesium chloride hexahydrate; 0.03 M Calcium chloride dihydrate); 0.1 M Buffer System 3 pH 8.5 (0.05 M Tris (base); 0.05 M BICINE); 30% v/v Precipitant Mix 1 (20% v/v PEG 500 MME; 10% w/v PEG 20000) and equilibrated versus 500 microL of reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.17 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.24 α = 90 b = 77.24 β = 90 c = 83.3 γ = 120
Symmetry Space Group P 31 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 PILATUS 6M 2022-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.000 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.06 66.89 100 0.09 0.022 0.999 18.16 17.51 18119 45.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.063 2.099 1.741 0.423 0.8554 2.212
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.06 66.89 1.35 18096 921 99.87 0.1944 0.192 0.1956 0.2392 0.2421
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.278 f_angle_d 0.91 f_chiral_restr 0.055 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2182 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing