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Aspergillus niger ferulic acid decarboxylase (Fdc)in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid, following decarboxylation (Int3')
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 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.89 α = 90 b = 64.21 β = 90 c = 87.57 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 2018-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.01 39.83 96.08 0.996 7.5 4.1 270737
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.01 1.046 82.3 0.536 1.07 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4ZA9 1.01 39.83 257321 13413 96.08 0.118 0.11703 0.13646 0.1492 RANDOM 11.879
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] -0.22 -0.05 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.838 r_sphericity_free 26.433 r_dihedral_angle_4_deg 20.787 r_dihedral_angle_3_deg 11.221 r_sphericity_bonded 9.488 r_dihedral_angle_1_deg 6.556 r_scbond_it 5.639 r_scbond_other 5.638 r_rigid_bond_restr 4.705 r_scangle_other 4.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.838 r_sphericity_free 26.433 r_dihedral_angle_4_deg 20.787 r_dihedral_angle_3_deg 11.221 r_sphericity_bonded 9.488 r_dihedral_angle_1_deg 6.556 r_scbond_it 5.639 r_scbond_other 5.638 r_rigid_bond_restr 4.705 r_scangle_other 4.299 r_long_range_B_refined 4.002 r_long_range_B_other 3.809 r_angle_refined_deg 2.021 r_mcangle_other 1.841 r_mcangle_it 1.838 r_mcbond_other 1.333 r_mcbond_it 1.332 r_angle_other_deg 1.256 r_chiral_restr 0.391 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 3846 Nucleic Acid Atoms Solvent Atoms 800 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling