☰ Navigation Tabs
Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant in complex with the covalent adduct formed between prFMN cofactor and 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 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.119 α = 90 b = 64.137 β = 90 c = 87.654 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 2018-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.969 Diamond I24
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 1.25 87.65 76.6 0.996 10.1 11.3 108947
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 1.25 1.282 0.581 1.8
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 FOURIER SYNTHESIS THROUGHOUT 4ZA9 1.25 87.65 108947 5848 76.56 0.13677 0.13502 0.1433 0.1698 0.1765 RANDOM 12.649
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] 0.08 -0.11 0.03
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.865 r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 21.659 r_sphericity_bonded 18.196 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 6.55 r_rigid_bond_restr 5.901 r_long_range_B_refined 5.466 r_long_range_B_other 5.462 r_scangle_other 4.168
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.865 r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 21.659 r_sphericity_bonded 18.196 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 6.55 r_rigid_bond_restr 5.901 r_long_range_B_refined 5.466 r_long_range_B_other 5.462 r_scangle_other 4.168 r_scbond_it 3.796 r_scbond_other 3.796 r_mcangle_other 2.914 r_mcangle_it 2.905 r_angle_refined_deg 2.753 r_mcbond_other 2.424 r_mcbond_it 2.359 r_angle_other_deg 1.338 r_chiral_restr 0.187 r_bond_refined_d 0.035 r_gen_planes_refined 0.031 r_bond_other_d 0.008 r_gen_planes_other 0.006 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 3852 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling