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Crystal structure of a Putative aldehyde dehydrogenase family protein Burkholderia cenocepacia J2315 in complex with partially reduced NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PXN Model identified with SIMBAD, MR done with 4pxnA as per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Molecular Dimensions Morpheus screen, H2: 10% PEG 8000, 20% EG: 20mM of each amino acid: sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MES / Imidazole pH 6.5: BuceA.00020.r.B1.PW37259 at 20mg/ml + 2.5mM NAD: cryo: direct: tray 299802h2: puck bit3-4
Crystal Properties Matthews coefficient Solvent content 2.73 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.67 α = 90 b = 124.98 β = 90 c = 246.2 γ = 90
Symmetry Space Group I 2 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 MX-300 2018-04-05 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 2.1 45.813 99.8 0.082 0.092 0.997 12.78 4.898 99329 29.36
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 2.1 2.15 100 0.507 0.566 0.863 3.08 5.062
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT Model identified with SIMBAD, MR done with 4pxnA as per MoRDa 2.1 45.813 1.34 99314 2040 99.84 0.1479 0.1471 0.1487 0.1893 0.1893 34.8319
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 11238 Nucleic Acid Atoms Solvent Atoms 1198 Heterogen Atoms 360
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction SIMBAD phasing MoRDa phasing Coot model building