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Feruloyl-CoA hydratase/lyase complexed with Vanillin and Coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Ammonium phosphate dibasic, Imidazole/Hydrochloric acid
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.471 α = 90 b = 132.471 β = 90 c = 241.533 γ = 120
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 270 2018-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.81 50 96.9 0.095 0.101 0.033 16.7 6.4 71335
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.84 89.4 0.324 0.383 0.198 0.444 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2j5i 1.81 30.65 67774 3561 96.78 0.2218 0.2201 0.254 0.2481 RANDOM 22.511
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.21 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_1_deg 7.031 r_angle_refined_deg 1.632 r_angle_other_deg 1.375 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.21 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_1_deg 7.031 r_angle_refined_deg 1.632 r_angle_other_deg 1.375 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3928 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-2000 data reduction