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C-terminal domain of pectobacterial FusB in complex with spinach ferredoxin 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZC8 experimental model PDB 1A70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05M HEPES,0.05M MOPS pH 7.5, 2M divalent cations (0.005M Manganese(II) chloride, 0.005M
Cobalt(II) chloride , 0.005M Nickel(II)
chloride, 0.005M Zinc acetate), 0.1 M monosaccharides (0.2 M xylitol, 0.2 M D-fructose, 0.2 M D-sorbitol, 0.2
M myo-inositol, 0.2 M L-rhamnose monohydrate), 20% PEGMME550, 10% PEG 20k
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.678 α = 90 b = 67.446 β = 90 c = 85.969 γ = 90
Symmetry Space Group C 2 2 21
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 XE 16M 2024-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.7 47.42 99.8 0.152 1 12.4 13.3 21660
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 1.156 0.8 1.4
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 1.7 47.42 20601 1026 99.68 0.16146 0.15923 0.1706 0.20536 0.2143 RANDOM 21.182
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] -0.62 2.08 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.58 r_long_range_B_refined 6.934 r_dihedral_angle_1_deg 6.797 r_long_range_B_other 6.787 r_dihedral_angle_2_deg 6.131 r_scangle_other 5.532 r_scbond_other 3.714 r_scbond_it 3.707 r_mcangle_other 2.757 r_mcangle_it 2.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.58 r_long_range_B_refined 6.934 r_dihedral_angle_1_deg 6.797 r_long_range_B_other 6.787 r_dihedral_angle_2_deg 6.131 r_scangle_other 5.532 r_scbond_other 3.714 r_scbond_it 3.707 r_mcangle_other 2.757 r_mcangle_it 2.755 r_mcbond_it 2.078 r_mcbond_other 2.073 r_angle_refined_deg 2.013 r_angle_other_deg 1.149 r_chiral_restr 0.113 r_gen_planes_other 0.018 r_gen_planes_refined 0.011 r_bond_refined_d 0.006 r_bond_other_d 0.002 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 1504 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing