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Crystal structure of AetF-L183F/V220I/S523A in complex with FAD and L-tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG 6000, 100 mM Tris pH 8.0, 10 mg/mL AetF-L183F/V220I/S523A (2 mM Trp, 5 mM DTT)
Crystal Properties Matthews coefficient Solvent content 2.1 41.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.481 α = 90 b = 74.863 β = 90 c = 142.247 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2025-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.28 25 98.8 0.087 0.096 0.041 0.997 11.5 5.2 29977
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.36 99.1 0.894 0.987 0.409 0.865 5.2
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 2.29 24.42 28443 1489 98.13 0.19628 0.19439 0.1988 0.23154 0.2368 RANDOM 50.666
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] 5.9 -4.55 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.526 r_dihedral_angle_4_deg 18.003 r_dihedral_angle_3_deg 16.958 r_long_range_B_refined 8.814 r_long_range_B_other 8.814 r_dihedral_angle_1_deg 7.514 r_scangle_other 6.38 r_mcangle_other 6.102 r_mcangle_it 6.1 r_mcbond_it 4.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.526 r_dihedral_angle_4_deg 18.003 r_dihedral_angle_3_deg 16.958 r_long_range_B_refined 8.814 r_long_range_B_other 8.814 r_dihedral_angle_1_deg 7.514 r_scangle_other 6.38 r_mcangle_other 6.102 r_mcangle_it 6.1 r_mcbond_it 4.161 r_mcbond_other 4.158 r_scbond_other 4.142 r_scbond_it 4.14 r_angle_refined_deg 1.51 r_angle_other_deg 1.24 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5188 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction