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Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei without cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287 BupsA.00020.b.AE1.PS38619 at 34.72 mg/mL against JCSG+ screen condition F7: 0.8 M succinate pH 7.0 supplemented with 20% ethylene glycol as cryo-protectant, unique puck ID gfm8-1, crystal tracking ID 314025f7
Crystal Properties Matthews coefficient Solvent content 3.69 66.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.86 α = 90 b = 107.86 β = 90 c = 233.53 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2020-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.05 49.51 99.9 0.094 0.101 0.998 12.86 7.085 51154 32.748
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 99.9 0.508 0.548 0.948 3.5 7.28
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2wox 2.05 49.51 49171 2932 96.08 0.1424 0.1404 0.1436 0.1729 0.1747 34.255
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3666 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 61
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction