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Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (NADPH bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8U9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 JCSG+ G8: 20% PEG 3350, 0.15 M DL-malic acid, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Plate: 13677, well G8 drop 1. Overnight soak with 5mM NADPH in crystallant. Puck: PSL-0503, Cryo: 30% PEG3350 + 70% crystallant
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.096 α = 90 b = 100.798 β = 95.79 c = 123.675 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 9M 2023-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.2 123.04 99.8 0.14 0.163 0.084 0.994 8.3 3.8 104034
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.9 1.187 1.379 0.695 0.5 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 83.67 1.34 103945 5117 99.68 0.1741 0.1719 0.2175 0.205
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 13.225 f_angle_d 0.904 f_chiral_restr 0.054 f_plane_restr 0.008 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14790 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 195
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing