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Structure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Recombinant protein with shortened C-terminal, in complex with NADP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 50 mM MOPS pH 7.5, 1.2 M ammonium sulfate, 1 mM NADP disodium salt
Crystal Properties Matthews coefficient Solvent content 3.85 68.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.23 α = 90 b = 105.23 β = 90 c = 315.28 γ = 90
Symmetry Space Group P 41 21 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 PILATUS3 S 6M 2017-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 99.93 97.33 0.5706 0.995 6.06 26.8 1862508 70248 41.0503127291
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.123 75.6 0.34
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 4WJ9 2.4 48.11 70235 2000 99.96 0.18411 0.1834 0.1927 0.20882 0.2161 RANDOM 43.06
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] 2.29 2.29 -4.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.726 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 13.873 r_dihedral_angle_1_deg 6.403 r_long_range_B_refined 5.791 r_long_range_B_other 5.783 r_scangle_other 4.355 r_mcangle_other 2.894 r_mcangle_it 2.893 r_scbond_it 2.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.726 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 13.873 r_dihedral_angle_1_deg 6.403 r_long_range_B_refined 5.791 r_long_range_B_other 5.783 r_scangle_other 4.355 r_mcangle_other 2.894 r_mcangle_it 2.893 r_scbond_it 2.746 r_scbond_other 2.737 r_mcbond_it 1.908 r_mcbond_other 1.908 r_angle_refined_deg 1.185 r_angle_other_deg 0.389 r_chiral_restr 0.049 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7974 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 253
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing