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Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NVM PDB ENTRY 1NVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 26-34% PEG 4000 or 3350, 0.1 M Tris, 0.2 M Li2SO4, 0.005M NAD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.88 α = 90 b = 92.21 β = 100.59 c = 56.48 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r 2011-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 43.35 97.6 0.059 13.68 3.98 424737 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 85.2 0.365 3.06 3.01
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 1NVM 1.55 25 3 424737 101394 5337 97.7 0.166 0.164 0.1895 0.2 0.2137 RANDOM 12.42
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] -0.66 1.03 -1.1 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.653 r_sphericity_free 19.495 r_dihedral_angle_4_deg 12.704 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 5.561 r_sphericity_bonded 5.316 r_rigid_bond_restr 2.673 r_angle_refined_deg 1.461 r_chiral_restr 0.099 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.653 r_sphericity_free 19.495 r_dihedral_angle_4_deg 12.704 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_1_deg 5.561 r_sphericity_bonded 5.316 r_rigid_bond_restr 2.673 r_angle_refined_deg 1.461 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4682 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 145
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling