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Crystal structure of AetD in complex with 5,7-dibromo-L-tryptophan and two Fe2+
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 0.01 M nickel chloride, 20% PEG 2000 MME, 0.1 M Tris, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.497 α = 90 b = 65.497 β = 90 c = 117.118 γ = 90
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 1.78 25 99.7 0.053 0.061 0.03 0.991 15.7 4.5 47258
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 1.78 1.84 100 0.675 0.758 0.341 0.835 4.8
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 1.78 23.44 44807 2407 99.54 0.19585 0.19327 0.2004 0.24361 0.2484 RANDOM 40.826
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] -1.12 -1.12 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.228 r_dihedral_angle_4_deg 21.179 r_dihedral_angle_3_deg 18.325 r_long_range_B_refined 8.021 r_long_range_B_other 8.021 r_scangle_other 6.376 r_dihedral_angle_1_deg 6.125 r_mcangle_it 4.361 r_mcangle_other 4.36 r_scbond_it 4.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.228 r_dihedral_angle_4_deg 21.179 r_dihedral_angle_3_deg 18.325 r_long_range_B_refined 8.021 r_long_range_B_other 8.021 r_scangle_other 6.376 r_dihedral_angle_1_deg 6.125 r_mcangle_it 4.361 r_mcangle_other 4.36 r_scbond_it 4.219 r_scbond_other 4.218 r_mcbond_it 3.241 r_mcbond_other 3.241 r_angle_refined_deg 1.591 r_angle_other_deg 1.419 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 3793 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing