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Wild-type Hydroxycinnamoyl-CoA hydratase lyase in complex with acetyl- CoA and vanillin
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 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.223 α = 90 b = 130.595 β = 90 c = 144.663 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 2007-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.22 97.13 91.5 0.12 9 5.2 73967 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 2.22 2.27 50.3 0.37 2.9 4.7
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 2.22 97.13 73967 3933 91.5 0.186 0.183 0.182 0.242 0.2405 RANDOM 37.85
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] -0.39 -1.84 2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.425 r_dihedral_angle_4_deg 22.714 r_dihedral_angle_3_deg 15.883 r_dihedral_angle_1_deg 6.949 r_scangle_it 4.142 r_scbond_it 2.861 r_angle_refined_deg 1.966 r_mcangle_it 1.58 r_mcbond_it 1.069 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.425 r_dihedral_angle_4_deg 22.714 r_dihedral_angle_3_deg 15.883 r_dihedral_angle_1_deg 6.949 r_scangle_it 4.142 r_scbond_it 2.861 r_angle_refined_deg 1.966 r_mcangle_it 1.58 r_mcbond_it 1.069 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.303 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.124 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 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 11344 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 215
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing