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Crystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei bound to cofactor NAD
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 8.5 287 BupsA.00020.b.AE1.PS38619 at 34.72 mg/mL with 4 mM NAD against Morpheus condition H11: 10% PEG 4000, 20% glycerol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL lysine, 0.02 M DL serine, 0.1 M bicine/Trizma pH 8.5, unique puck ID qvy9-3, 314030h11
Crystal Properties Matthews coefficient Solvent content 2.79 55.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.27 α = 90 b = 156.7 β = 90 c = 76.23 γ = 90
Symmetry Space Group P 21 21 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 1.55 43.09 99.9 0.076 0.083 0.999 16.47 6.123 172302 20.398
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 1.55 1.59 100 0.566 0.621 0.871 3.02 6.003
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 1.55 43.09 166209 10050 96.41 0.1459 0.1444 0.1457 0.1685 0.1681 17.3817
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 7322 Nucleic Acid Atoms Solvent Atoms 1388 Heterogen Atoms 100
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction