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Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VLE 2VLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 protein conditions: 8 mg/ml recombinant ALDH2 in 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM DTT, supplemented with 2-4% v/v DMSO
well conditions: 100 mM sodium citrate, pH 5.0-5.6, 22-26% w/v PEG MME 550 550
hanging drops were set with a 1.5:1 protein:well ratio
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.961 α = 90 b = 119.961 β = 90 c = 135.287 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS EIGER X 16M 2022-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.984 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 49.92 99.9 0.999 16.37 13.5 155768
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 99.6 0.809 13.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 2VLE 1.5 49.92 147935 7832 99.91 0.1369 0.1358 0.1362 0.1574 0.1354 RANDOM 15.868
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] 0.47 0.47 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.52 r_dihedral_angle_2_deg 12.366 r_dihedral_angle_1_deg 6.774 r_angle_refined_deg 1.741 r_angle_other_deg 0.589 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7600 Nucleic Acid Atoms Solvent Atoms 941 Heterogen Atoms 280
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction