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Structure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Native protein)
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 and 1.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.72 66.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.29 α = 90 b = 105.29 β = 90 c = 314.45 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) 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 2.25 48.08 99.97 0.5602 0.09949 0.985 12.1 30.3 84880 41.3327863925
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 2.25 2.33 99.99 2.21 26.6
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 2.25 48.04 82881 2000 99.98 0.18905 0.18856 0.1946 0.20951 0.2156 RANDOM 43.588
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] 1.78 1.78 -3.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.784 r_dihedral_angle_4_deg 16.68 r_dihedral_angle_3_deg 13.743 r_long_range_B_refined 6.314 r_long_range_B_other 6.246 r_dihedral_angle_1_deg 5.933 r_scangle_other 5.4 r_scbond_it 3.444 r_scbond_other 3.423 r_mcangle_other 3.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.784 r_dihedral_angle_4_deg 16.68 r_dihedral_angle_3_deg 13.743 r_long_range_B_refined 6.314 r_long_range_B_other 6.246 r_dihedral_angle_1_deg 5.933 r_scangle_other 5.4 r_scbond_it 3.444 r_scbond_other 3.423 r_mcangle_other 3.228 r_mcangle_it 3.227 r_mcbond_it 2.212 r_mcbond_other 2.211 r_angle_refined_deg 0.836 r_angle_other_deg 0.293 r_chiral_restr 0.036 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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 8272 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing