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A. vinelandii Fe-nitrogenase FeFe protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Bis Tris propane/HCl at pH 8.5
18 % (w/v) of polyethylene glycol 4000
18 % (v/v) of ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.68 53.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.969 α = 90 b = 151.048 β = 90 c = 158.863 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
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 1.547 20.1 39.9 0.109 0.031 0.995 14.9 1.9 153829 21.98
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 1.55 1.75 70.4 1.285 0.387 0.662 2.1 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5N6Y 1.547 20.003 153828 7578 91.8 0.171 0.1688 0.1797 0.2155 0.2244 27.129
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] -0.12 0.042 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.232 r_dihedral_angle_3_deg 14.947 r_dihedral_angle_other_3_deg 9.471 r_lrange_it 8.956 r_lrange_other 8.852 r_dihedral_angle_2_deg 8.154 r_dihedral_angle_1_deg 7.185 r_scangle_it 3.474 r_scangle_other 3.474 r_mcangle_it 2.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.232 r_dihedral_angle_3_deg 14.947 r_dihedral_angle_other_3_deg 9.471 r_lrange_it 8.956 r_lrange_other 8.852 r_dihedral_angle_2_deg 8.154 r_dihedral_angle_1_deg 7.185 r_scangle_it 3.474 r_scangle_other 3.474 r_mcangle_it 2.921 r_mcangle_other 2.921 r_scbond_it 2.203 r_scbond_other 2.203 r_mcbond_it 1.917 r_mcbond_other 1.916 r_angle_refined_deg 1.339 r_angle_other_deg 0.446 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.177 r_nbd_other 0.175 r_symmetry_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.106 r_metal_ion_refined 0.1 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.065 r_chiral_restr_other 0.025 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17320 Nucleic Acid Atoms Solvent Atoms 1428 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building