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Crystal structure of a NAD-dependent Aldehyde dehydrogenase from Burkholderia multivorans in covalent complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 Molecular Dimensions Morpheus screen G7: 10% PEG 4000, 20% Glycerol, 20mM of each: Na-formate, Ammonium-acetate, Trisodium citrate, Na/K tartrate, Na oxamate; 100mM MOPS/NaHEPES pH 7.5; BumuA.00020.x.B1.PS37849 at 20mg/ml + 2mM NADP; cryo: direct, puck pfb1-6, tray 271259 g7
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.08 α = 90 b = 87.03 β = 90 c = 124.59 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 2016-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 50 100 0.08 0.999 15.71 8 147035 -3 8.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.23 100 0.551 3.32
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3pqa 1.2 50 1.35 147020 1964 99.98 0.113 0.1128 0.1135 0.1297 0.1318 RANDOM 11.7957
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 17.035 f_angle_d 1.064 f_chiral_restr 0.082 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3607 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 112
Software Software Software Name Purpose XDS data scaling XSCALE data scaling PHASER phasing Coot model building PHENIX model building PHENIX refinement PDB_EXTRACT data extraction