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Crystal structure of AetD in complex with 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 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.353 α = 90 b = 65.353 β = 90 c = 117.269 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 1.61 25 99.5 0.037 0.042 0.019 0.996 22.7 5 63234
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 1.61 1.67 99.8 0.623 0.689 0.293 0.845 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.61 23.42 59359 3109 98.36 0.22384 0.22109 0.27563 0.2835 RANDOM 20.334
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.299 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 16.706 r_dihedral_angle_1_deg 6.286 r_long_range_B_refined 5.563 r_long_range_B_other 5.372 r_scangle_other 3.423 r_mcangle_it 2.547 r_mcangle_other 2.547 r_scbond_it 2.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.299 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 16.706 r_dihedral_angle_1_deg 6.286 r_long_range_B_refined 5.563 r_long_range_B_other 5.372 r_scangle_other 3.423 r_mcangle_it 2.547 r_mcangle_other 2.547 r_scbond_it 2.138 r_scbond_other 2.137 r_angle_refined_deg 1.663 r_mcbond_it 1.657 r_mcbond_other 1.657 r_angle_other_deg 1.405 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 3803 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing