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Aspergillus niger ferulic acid decarboxylase (Fdc) S145C-P289C (DB2) variant in complex with prenylated flavin hydroxylated at the C1 prime position
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 BIS-TRIS propane, potassium thiocyanate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.879 α = 90 b = 63.995 β = 90 c = 87.708 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 EIGER2 XE 16M 2021-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.37 87.71 98 1 10.9 12.9 1458231
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 1.37 1.39 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.37 87.71 88815 4675 81.98 0.15152 0.15074 0.1506 0.166 0.1663 RANDOM 13.772
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 0.07 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.391 r_dihedral_angle_2_deg 11.115 r_dihedral_angle_1_deg 6.485 r_long_range_B_refined 5.132 r_long_range_B_other 5.132 r_scangle_other 3.06 r_scbond_other 2.13 r_scbond_it 2.129 r_mcangle_it 1.826 r_mcangle_other 1.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.391 r_dihedral_angle_2_deg 11.115 r_dihedral_angle_1_deg 6.485 r_long_range_B_refined 5.132 r_long_range_B_other 5.132 r_scangle_other 3.06 r_scbond_other 2.13 r_scbond_it 2.129 r_mcangle_it 1.826 r_mcangle_other 1.826 r_angle_refined_deg 1.748 r_mcbond_it 1.266 r_mcbond_other 1.265 r_angle_other_deg 0.604 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3846 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing