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Crystal structure of FutA bound to Fe(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 294 Purified protein and crystallisation buffer were mixed at a 1:1 ratio. Crystallisation buffer was 20% PEG 3350, 200 mM sodium thiocyanate.
Crystal Properties Matthews coefficient Solvent content 2.07 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.361 α = 90 b = 78.011 β = 98.226 c = 47.994 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 294 PIXEL RIGAKU HyPix-6000HE 2018-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.7 47.5 97.9 0.053 0.054 0.009 1 71.7 65.4 30881
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 1.7 1.73 83.5 0.403 0.412 0.085 0.986 11.6 42.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 47.5 30847 1588 97.67 0.155 0.1532 0.1626 0.1804 0.1878 19.081
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] 0.013 -0.217 0.464 -0.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.871 r_dihedral_angle_4_deg 18.149 r_dihedral_angle_3_deg 14.341 r_lrange_other 6.708 r_lrange_it 6.702 r_dihedral_angle_1_deg 6.054 r_scangle_it 5.735 r_scangle_other 5.734 r_scbond_it 3.657 r_scbond_other 3.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.871 r_dihedral_angle_4_deg 18.149 r_dihedral_angle_3_deg 14.341 r_lrange_other 6.708 r_lrange_it 6.702 r_dihedral_angle_1_deg 6.054 r_scangle_it 5.735 r_scangle_other 5.734 r_scbond_it 3.657 r_scbond_other 3.655 r_mcangle_it 2.711 r_mcangle_other 2.711 r_mcbond_it 2.001 r_mcbond_other 1.994 r_angle_refined_deg 1.879 r_angle_other_deg 1.516 r_nbd_other 0.218 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.167 r_xyhbond_nbd_refined 0.16 r_metal_ion_refined 0.09 r_chiral_restr 0.088 r_symmetry_xyhbond_nbd_other 0.086 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2464 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing