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Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with prFMN (purified in dark) and alphafluorocinnamic acid
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 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS
PROPANE 6.5, 20 % W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.681 α = 90 b = 63.945 β = 90 c = 87.573 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 2018-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.916 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.103 51.64 88.4 0.065 0.998 10.7 5 190502
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.103 1.142 61.06 0.58 0.702 2 4.3
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 1.13 51.64 180930 9574 88.39 0.12027 0.11911 0.1277 0.14184 0.1488 RANDOM 12.889
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] 0.63 -1.19 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.055 r_sphericity_free 23.565 r_dihedral_angle_4_deg 20.836 r_sphericity_bonded 12.412 r_dihedral_angle_3_deg 12.009 r_rigid_bond_restr 11.242 r_dihedral_angle_1_deg 6.613 r_long_range_B_refined 4.135 r_scbond_it 4.102 r_scbond_other 4.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.055 r_sphericity_free 23.565 r_dihedral_angle_4_deg 20.836 r_sphericity_bonded 12.412 r_dihedral_angle_3_deg 12.009 r_rigid_bond_restr 11.242 r_dihedral_angle_1_deg 6.613 r_long_range_B_refined 4.135 r_scbond_it 4.102 r_scbond_other 4.102 r_long_range_B_other 4.079 r_scangle_other 3.805 r_mcbond_other 2.538 r_mcbond_it 2.536 r_mcangle_other 2.424 r_mcangle_it 2.418 r_angle_refined_deg 1.891 r_angle_other_deg 1.174 r_chiral_restr 0.312 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 3847 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling