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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 4LRS pdb entry 4LRS
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, 0.005 M CoA, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.5 α = 90 b = 116.7 β = 90 c = 131.5 γ = 90
Symmetry Space Group P 21 21 21
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 0.8856 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 1.5 46.45 90 0.033 22.53 3.89 208563 812171 3 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 1.5 1.54 52.5 0.428 3.04 3.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4LRS 1.5 46.45 208563 198134 10429 100 0.15234 0.15139 0.1576 0.17016 0.1769 RANDOM 19.556
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] -0.96 0.23 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.919 r_dihedral_angle_4_deg 14.32 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 5.573 r_scangle_it 2.882 r_scbond_it 1.759 r_angle_refined_deg 1.334 r_mcangle_it 1.021 r_mcbond_it 0.595 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.919 r_dihedral_angle_4_deg 14.32 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 5.573 r_scangle_it 2.882 r_scbond_it 1.759 r_angle_refined_deg 1.334 r_mcangle_it 1.021 r_mcbond_it 0.595 r_chiral_restr 0.14 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9307 Nucleic Acid Atoms Solvent Atoms 1364 Heterogen Atoms 142
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling