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Structure of YIUA from Yersinia ruckeri with iron
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 0,2 M sodium nitrate; 0.1 M Bis-Tris propane pH 6.5; 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.494 α = 90 b = 76.228 β = 95.06 c = 99.926 γ = 90
Symmetry Space Group P 1 21 1
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 0.75166 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 2.32 60.59 100 0.12 0.09 0.99 5.9 6.2 60167
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 2.32 2.38 0.99 0.7 0.73 1
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 2.32 60.59 57179 2944 99.9 0.2463 0.24419 0.2502 0.28669 0.2886 RANDOM 39.616
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] -1.9 0.88 5.97 -4.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.854 r_dihedral_angle_2_deg 10.424 r_long_range_B_refined 8.362 r_long_range_B_other 8.361 r_dihedral_angle_1_deg 6.838 r_mcangle_it 5.875 r_mcangle_other 5.874 r_scangle_other 5.779 r_mcbond_it 3.755 r_mcbond_other 3.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.854 r_dihedral_angle_2_deg 10.424 r_long_range_B_refined 8.362 r_long_range_B_other 8.361 r_dihedral_angle_1_deg 6.838 r_mcangle_it 5.875 r_mcangle_other 5.874 r_scangle_other 5.779 r_mcbond_it 3.755 r_mcbond_other 3.753 r_scbond_it 3.564 r_scbond_other 3.564 r_angle_refined_deg 1.519 r_angle_other_deg 0.542 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 10051 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing