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Aspergillus niger ferulic acid decarboxylase (Fdc) L439G variant in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid (Int1')
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 2.41 48.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.01 α = 90 b = 64.37 β = 90 c = 87.81 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 1.12 39.93 99.25 0.997 7.95 4.3 207057
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 1.12 1.16 0.59 1.32
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 1.12 39.93 196709 10348 99.26 0.12556 0.12422 0.124 0.15046 0.1506 RANDOM 13.429
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] -0.23 -0.17 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.194 r_sphericity_free 25.916 r_dihedral_angle_4_deg 20.427 r_dihedral_angle_3_deg 11.963 r_sphericity_bonded 9.766 r_dihedral_angle_1_deg 6.56 r_rigid_bond_restr 4.978 r_long_range_B_refined 3.771 r_scangle_other 3.417 r_scbond_it 3.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.194 r_sphericity_free 25.916 r_dihedral_angle_4_deg 20.427 r_dihedral_angle_3_deg 11.963 r_sphericity_bonded 9.766 r_dihedral_angle_1_deg 6.56 r_rigid_bond_restr 4.978 r_long_range_B_refined 3.771 r_scangle_other 3.417 r_scbond_it 3.363 r_scbond_other 3.361 r_long_range_B_other 3.063 r_angle_refined_deg 2.031 r_mcangle_other 1.885 r_mcangle_it 1.884 r_mcbond_it 1.505 r_mcbond_other 1.505 r_angle_other_deg 1.248 r_chiral_restr 0.396 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 3850 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling