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Crystal structure of AetF in complex with FAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG 6000, 0.1 M Tris pH 8.0, 8 mg/mL AetF (5 mM DTT)
Crystal Properties Matthews coefficient Solvent content 2.06 40.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.475 α = 90 b = 74.963 β = 90 c = 143.099 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 9M 2023-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
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 1.85 25 96.1 0.045 0.051 0.023 1 14.3 4.5 54003
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 1.85 1.92 89.6 0.435 0.484 0.208 0.894 4.5
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 1.85 24.47 51217 2724 95.85 0.18024 0.17768 0.1853 0.22925 0.2363 RANDOM 33.164
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] 3.21 -1.81 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.604 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_4_deg 15.731 r_long_range_B_refined 7.399 r_long_range_B_other 7.37 r_dihedral_angle_1_deg 7.097 r_scangle_other 5.421 r_mcangle_it 4.156 r_mcangle_other 4.156 r_scbond_other 3.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.604 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_4_deg 15.731 r_long_range_B_refined 7.399 r_long_range_B_other 7.37 r_dihedral_angle_1_deg 7.097 r_scangle_other 5.421 r_mcangle_it 4.156 r_mcangle_other 4.156 r_scbond_other 3.501 r_scbond_it 3.499 r_mcbond_it 2.947 r_mcbond_other 2.944 r_angle_refined_deg 1.532 r_angle_other_deg 1.346 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 5207 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing