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Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD bound, orthorhombic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 291 JCSG+ D12: 0.04 M Pottasium Phosphate, 16% PEG 8K, 20% Glycerol. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: 13164, well D12 drop 2, Puck: PSL-0615, Cryo: Direct. Subunits C and D contain NAD. Subunits A and B have interlaced alternate conformations from residues 180-196 and were refined with partial occupancies
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.97 α = 90 b = 91.942 β = 90 c = 144.165 γ = 90
Symmetry Space Group P 21 21 21
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 2022-02-14 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 1.8 91.94 100 0.122 0.127 0.035 0.998 13 12.8 89308
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 1.8 1.85 100 1.419 1.478 0.412 0.765 12.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.81 42.59 1.32 86711 4315 99.22 0.1711 0.1693 0.1785 0.2051 0.2133
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 13.179 f_angle_d 0.637 f_chiral_restr 0.046 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7169 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing