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Crystal structure of AetF in complex with FAD and NADP+ at 1.86 angstrom
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 2.05 40.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.425 α = 90 b = 75.447 β = 90 c = 143.845 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 2023-06-30 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 1.86 25 99.1 0.061 0.068 0.031 0.999 11.3 4.6 55009
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 1.86 1.93 99.6 0.397 0.45 0.206 0.911 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 1.86 24.79 52155 2790 98.48 0.18376 0.18085 0.1885 0.2385 0.2415 RANDOM 35.716
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] 3.5 -2.81 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.447 r_dihedral_angle_3_deg 17.166 r_dihedral_angle_4_deg 16.051 r_long_range_B_refined 8.242 r_long_range_B_other 8.231 r_dihedral_angle_1_deg 7.258 r_scangle_other 5.663 r_mcangle_it 4.164 r_mcangle_other 4.164 r_scbond_it 3.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.447 r_dihedral_angle_3_deg 17.166 r_dihedral_angle_4_deg 16.051 r_long_range_B_refined 8.242 r_long_range_B_other 8.231 r_dihedral_angle_1_deg 7.258 r_scangle_other 5.663 r_mcangle_it 4.164 r_mcangle_other 4.164 r_scbond_it 3.682 r_scbond_other 3.682 r_mcbond_it 2.994 r_mcbond_other 2.993 r_angle_refined_deg 1.541 r_angle_other_deg 1.32 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 5209 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing