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Structure of A. niger Fdc Wt in complex with FMN and benzothiophene 2 carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.39 α = 90 b = 63.283 β = 90 c = 87.501 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 6M-F 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) Rrim I (All) 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 1.54 95.57 99.8 0.136 1 6.9 5 78889
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 0.816 0.5 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 4ZAA 1.54 64.482 78838 3869 99.736 0.15 0.1479 0.1621 0.1951 0.2046 18.2
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] 0.328 -0.449 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.54 r_dihedral_angle_4_deg 22.344 r_dihedral_angle_3_deg 12.437 r_dihedral_angle_1_deg 6.788 r_lrange_it 4.663 r_lrange_other 4.662 r_rigid_bond_restr 3.838 r_scangle_it 3.745 r_scangle_other 3.742 r_mcangle_other 3.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.54 r_dihedral_angle_4_deg 22.344 r_dihedral_angle_3_deg 12.437 r_dihedral_angle_1_deg 6.788 r_lrange_it 4.663 r_lrange_other 4.662 r_rigid_bond_restr 3.838 r_scangle_it 3.745 r_scangle_other 3.742 r_mcangle_other 3.405 r_mcangle_it 3.404 r_scbond_it 3.291 r_scbond_other 3.291 r_mcbond_it 2.841 r_mcbond_other 2.835 r_angle_refined_deg 1.98 r_angle_other_deg 1.59 r_symmetry_nbd_refined 0.245 r_nbd_refined 0.239 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_other 0.222 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.171 r_chiral_restr 0.113 r_metal_ion_refined 0.102 r_symmetry_nbtor_other 0.085 r_symmetry_metal_ion_refined 0.076 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3807 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling