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Crystal structure of AetF-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-V220I/S523A (2 mM Trp, 5 mM DTT)
Crystal Properties Matthews coefficient Solvent content 2.1 41.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.234 α = 90 b = 75.423 β = 90 c = 143.764 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 PIXEL DECTRIS EIGER2 X 16M 2024-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97621 NSRRC TPS 07A
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 2.32 25 98.1 0.092 0.107 0.052 0.996 6.9 4.4 28435
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 2.32 2.4 99.9 0.617 0.703 0.331 0.868 4.3
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 2.32 24.78 26945 1438 96.93 0.22228 0.21824 0.221 0.29491 0.2935 RANDOM 55.478
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] 7.27 -4.05 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.455 r_dihedral_angle_3_deg 18.159 r_dihedral_angle_4_deg 15.774 r_long_range_B_other 8.403 r_long_range_B_refined 8.401 r_dihedral_angle_1_deg 7.125 r_scangle_other 6.157 r_mcangle_it 5.927 r_mcangle_other 5.927 r_mcbond_other 4.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.455 r_dihedral_angle_3_deg 18.159 r_dihedral_angle_4_deg 15.774 r_long_range_B_other 8.403 r_long_range_B_refined 8.401 r_dihedral_angle_1_deg 7.125 r_scangle_other 6.157 r_mcangle_it 5.927 r_mcangle_other 5.927 r_mcbond_other 4.081 r_mcbond_it 4.08 r_scbond_it 4.042 r_scbond_other 4.041 r_angle_refined_deg 1.44 r_angle_other_deg 1.17 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 5202 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction