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Structure of YIUA from Yersinia ruckeri with Iron and nitrilotriacetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 12.5% (w/v) PEG 1000; 12.5% (w/v) PEG 3350; 12.5% (v/v) MPD; 0.02 M alcohols; 0.1 M MES/imidazole pH 6.5 (Molecular Dimensions Morpheus D4)
Crystal Properties Matthews coefficient Solvent content 1.97 37.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.146 α = 101.36 b = 59.386 β = 94.49 c = 101.171 γ = 100.54
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS EIGER2 XE 16M 2024-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.77296 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.14 54.78 98.9 0.17 0.17 0.98 4.4 3.7 47589
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.2 0.96 0.96 0.57 1.2
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 2.14 54.78 45243 2329 98.88 0.20728 0.20501 0.25343 0.2472 RANDOM 32.149
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] 0.41 0.65 1.98 -2.98 0.12 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.136 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 7.49 r_long_range_B_other 7.03 r_long_range_B_refined 7.029 r_scangle_other 5.292 r_mcangle_it 4.669 r_mcangle_other 4.666 r_scbond_other 3.483 r_scbond_it 3.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.136 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 7.49 r_long_range_B_other 7.03 r_long_range_B_refined 7.029 r_scangle_other 5.292 r_mcangle_it 4.669 r_mcangle_other 4.666 r_scbond_other 3.483 r_scbond_it 3.482 r_mcbond_it 3.192 r_mcbond_other 3.189 r_angle_refined_deg 1.629 r_angle_other_deg 0.57 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 7497 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing