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Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) 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 = 95.78 α = 90 b = 64.03 β = 90 c = 87.59 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 1.35 53.29 93.5 1 13.7 13.3 110958
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 1.35 1.37 59.6 0.3 10.6
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 1.35 53.29 105313 5601 93.49 0.15325 0.15206 0.1602 0.17596 0.1825 RANDOM 17.14
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] -0.9 1.09 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.43 r_dihedral_angle_2_deg 11.31 r_dihedral_angle_1_deg 6.559 r_long_range_B_refined 4.626 r_long_range_B_other 4.626 r_scangle_other 3.276 r_scbond_it 2.384 r_scbond_other 2.38 r_mcangle_it 2.103 r_mcangle_other 2.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.43 r_dihedral_angle_2_deg 11.31 r_dihedral_angle_1_deg 6.559 r_long_range_B_refined 4.626 r_long_range_B_other 4.626 r_scangle_other 3.276 r_scbond_it 2.384 r_scbond_other 2.38 r_mcangle_it 2.103 r_mcangle_other 2.102 r_angle_refined_deg 1.78 r_mcbond_it 1.536 r_mcbond_other 1.507 r_angle_other_deg 0.615 r_chiral_restr 0.099 r_gen_planes_refined 0.012 r_bond_refined_d 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 3854 Nucleic Acid Atoms Solvent Atoms 552 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing