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Structure of A. niger Fdc WT in complex with FMN and indole 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 2.39 48.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.894 α = 90 b = 63.934 β = 90 c = 87.668 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 2018-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.975 Diamond I04
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 1.28 64.79 100 0.12 1 8.5 6.4 139040
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 1.28 1.3 98.9 0.818 0.5 1.8
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 1.28 64.704 137282 6826 98.717 0.162 0.1604 0.1603 0.1976 0.1978 11.866
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] 0.117 -0.174 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.6 r_dihedral_angle_4_deg 21.753 r_dihedral_angle_3_deg 12.341 r_dihedral_angle_1_deg 6.776 r_rigid_bond_restr 4.981 r_lrange_it 3.999 r_lrange_other 3.999 r_scangle_it 3.33 r_scangle_other 3.329 r_scbond_it 2.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.6 r_dihedral_angle_4_deg 21.753 r_dihedral_angle_3_deg 12.341 r_dihedral_angle_1_deg 6.776 r_rigid_bond_restr 4.981 r_lrange_it 3.999 r_lrange_other 3.999 r_scangle_it 3.33 r_scangle_other 3.329 r_scbond_it 2.931 r_scbond_other 2.931 r_mcangle_it 2.415 r_mcangle_other 2.414 r_angle_refined_deg 2.223 r_mcbond_it 2.065 r_mcbond_other 2.065 r_angle_other_deg 1.681 r_nbd_refined 0.247 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_other 0.225 r_symmetry_nbd_refined 0.215 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.129 r_metal_ion_refined 0.119 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.039 r_symmetry_metal_ion_refined 0.022 r_bond_refined_d 0.019 r_gen_planes_refined 0.017 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3807 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling