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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, ADH508)
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
Crystal Properties Matthews coefficient Solvent content 3.88 68.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.19 α = 90 b = 105.19 β = 90 c = 314.57 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 PILATUS 6M-F 2016-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.23 99.7200568611 86.76 0.36 0.13 0.98 4.41 6.4 39303 51.9054394987
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 2.23 2.316
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 2.9 48.04 37301 2000 97.72 0.19192 0.18993 0.2012 0.22864 0.2344 RANDOM 55.192
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] 2.82 2.82 -5.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.405 r_dihedral_angle_4_deg 19.333 r_dihedral_angle_3_deg 17.467 r_long_range_B_refined 9.973 r_long_range_B_other 9.97 r_scangle_other 7.224 r_dihedral_angle_1_deg 7.205 r_mcangle_it 5.578 r_mcangle_other 5.578 r_scbond_it 4.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.405 r_dihedral_angle_4_deg 19.333 r_dihedral_angle_3_deg 17.467 r_long_range_B_refined 9.973 r_long_range_B_other 9.97 r_scangle_other 7.224 r_dihedral_angle_1_deg 7.205 r_mcangle_it 5.578 r_mcangle_other 5.578 r_scbond_it 4.727 r_scbond_other 4.676 r_mcbond_it 3.683 r_mcbond_other 3.683 r_angle_refined_deg 1.52 r_angle_other_deg 0.499 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 7900 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing