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Crystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 100 mM bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-TRIS), 25% PEG 3350, 60 mM urea;
13.3 mM magnesium chloride, 8.9 mM tris(2-carboxyethyl)phosphine (TCEP), 4.4 mM NAD+, 45.8 mM glucose, crystals have been soaked with glyceryl trinitrate (GTN), pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.862 α = 90 b = 148.431 β = 90 c = 176.005 γ = 90
Symmetry Space Group C 2 2 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 CCD MAR CCD 165 mm 2010-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81230 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.281 19.83 99.1 0.082 0.082 14.5 6.4 521666 81819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.39 99.9 0.295 0.295 5.7 6.4
Refinement Statistics Diffraction ID Structure Solution 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 1o05 2.281 19.802 1.34 80015 4023 98.33 0.1719 0.1699 0.1628 0.2092 0.2019 Random
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] 2.0467 -0.1382 -1.9086
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.077 f_angle_d 0.889 f_chiral_restr 0.058 f_bond_d 0.012 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15138 Nucleic Acid Atoms Solvent Atoms 889 Heterogen Atoms 220
Software Software Software Name Purpose DNA data collection PHASER phasing PHENIX refinement XDS data reduction SCALA data scaling