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Crystal structure of NAD-dependent aldehyde dehydrogenase from Burkholderia multivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RJL PDB entry 3rjl
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 RigakuReagents JCSG+ screen, E1: 100mM Sodium citrate tribasic, 100mM Sodium cocodylate/HCl pH 6.5: BumuA.00020.h.B1.PS37903 at 19.95mg/ml + 2mM NAD: cryo: 20% EG + 2mM NAD: tray 272909e1, puck LCP4-1. Imidazole tentatively modeled, it was present during purification.
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.43 α = 90 b = 114.43 β = 90 c = 154.52 γ = 120
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 2016-11-09 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 50 99.5 0.085 0.089 0.998 15.61 8.688 71387 -3 31.07
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 0.522 0.553 0.943 3.37 8.647 5285
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 FREE R-VALUE PDB entry 3rjl 2.05 47.183 1.34 71301 1990 99.42 0.1496 0.1482 0.151 0.1967 0.1996 38.0455
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 11.156 f_angle_d 0.788 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8314 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 32
Software Software Software Name Purpose XSCALE data scaling XDS data reduction PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing Coot model building BALBES phasing MOLREP phasing