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Crystal structure of AetD in complex with 5-bromo-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 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.633 α = 90 b = 65.633 β = 90 c = 117.313 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 2023-04-16 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 2.01 25 97.6 0.028 0.032 0.016 0.998 23.1 3.9 32155
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 2.01 2.08 92.5 0.488 0.574 0.298 0.822 3.3
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 2.01 22.77 30097 1532 96.03 0.20909 0.20588 0.2127 0.27333 0.2757 RANDOM 30.389
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] -0.27 -0.27 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.18 r_dihedral_angle_3_deg 18.1 r_dihedral_angle_4_deg 17.54 r_long_range_B_refined 6.4 r_long_range_B_other 6.391 r_dihedral_angle_1_deg 6.167 r_scangle_other 4.437 r_mcangle_it 3.508 r_mcangle_other 3.508 r_scbond_it 2.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.18 r_dihedral_angle_3_deg 18.1 r_dihedral_angle_4_deg 17.54 r_long_range_B_refined 6.4 r_long_range_B_other 6.391 r_dihedral_angle_1_deg 6.167 r_scangle_other 4.437 r_mcangle_it 3.508 r_mcangle_other 3.508 r_scbond_it 2.772 r_scbond_other 2.772 r_mcbond_it 2.263 r_mcbond_other 2.263 r_angle_refined_deg 1.515 r_angle_other_deg 1.345 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 3808 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing