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A ternary complex of Hydroxycinnamoyl-CoA Hydratase-Lyase (HCHL) with acetyl-Coenzyme A and vanillin gives insights into substrate specificity and mechanism.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J5I PDB ENTRY 2J5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID BUFFER PH 5.6. 10MM FERULOYL-COA.
Crystal Properties Matthews coefficient Solvent content 2.3 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.081 α = 90 b = 130.122 β = 90 c = 144.743 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 287 CCD ADSC CCD 2007-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.9 96.67 96.7 0.1 6.8 5.5 123802 2
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 1.9 1.95 76.8 0.69 2.5 2.9
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 PDB ENTRY 2J5I 1.9 96.67 123802 6562 96.7 0.191 0.188 0.1898 0.23 0.2324 RANDOM 25.38
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] -1.14 -1.26 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.879 r_dihedral_angle_4_deg 21.336 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.079 r_scangle_it 3.519 r_scbond_it 2.427 r_angle_refined_deg 1.635 r_mcangle_it 1.338 r_mcbond_it 0.943 r_symmetry_hbond_refined 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.879 r_dihedral_angle_4_deg 21.336 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.079 r_scangle_it 3.519 r_scbond_it 2.427 r_angle_refined_deg 1.635 r_mcangle_it 1.338 r_mcbond_it 0.943 r_symmetry_hbond_refined 0.353 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 11496 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing