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Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant in complex with the covalent adduct formed between prFMN cofactor and alphafluoro-cinnamic acid (Int2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS
PROPANE 6.5, 20 % W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.132 α = 90 b = 64.054 β = 90 c = 87.748 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 300K 2018-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.13 64.81 99.8 11.93 4.8 201927
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.17 98.5 3.01
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 FOURIER SYNTHESIS THROUGHOUT 4ZA9 1.13 64.81 191901 10104 99.8 0.121 0.12 0.139 0.1537 RANDOM 11.92
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.245 r_dihedral_angle_4_deg 21.139 r_sphericity_free 15.349 r_dihedral_angle_3_deg 12.305 r_rigid_bond_restr 8.727 r_dihedral_angle_1_deg 6.727 r_sphericity_bonded 6.216 r_scbond_other 3.029 r_scbond_it 3.026 r_scangle_other 3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.245 r_dihedral_angle_4_deg 21.139 r_sphericity_free 15.349 r_dihedral_angle_3_deg 12.305 r_rigid_bond_restr 8.727 r_dihedral_angle_1_deg 6.727 r_sphericity_bonded 6.216 r_scbond_other 3.029 r_scbond_it 3.026 r_scangle_other 3.01 r_angle_refined_deg 2.98 r_long_range_B_refined 2.902 r_long_range_B_other 2.902 r_mcangle_it 2.011 r_mcangle_other 2.011 r_mcbond_other 1.83 r_mcbond_it 1.824 r_angle_other_deg 1.636 r_chiral_restr 0.19 r_bond_refined_d 0.034 r_gen_planes_refined 0.028 r_gen_planes_other 0.011 r_bond_other_d 0.005 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3842 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling