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CO bound as bridging ligand at the active site of vanadium nitrogenase VFe protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Tris/HCl pH 7.5, magnesium chloride, ethylene glycol, PEG 8000, sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.579 α = 84.11 b = 79.934 β = 72.42 c = 107.223 γ = 75.19
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 2018-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.849205 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 48.45 88.1 0.998 10.6 7.6 1101498
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.02 0.592
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 (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 6FEA 1 48.45 1095802 5649 88.13 0.1019 0.1019 0.1018 0.1169 0.1167 RANDOM 14.169
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] 0.27 0.22 0.55 0.69 -0.17 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.599 r_dihedral_angle_1_deg 20.256 r_dihedral_angle_4_deg 18.827 r_dihedral_angle_3_deg 12.25 r_rigid_bond_restr 8.779 r_angle_refined_deg 3.154 r_angle_other_deg 1.874 r_chiral_restr 0.493 r_bond_refined_d 0.023 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.599 r_dihedral_angle_1_deg 20.256 r_dihedral_angle_4_deg 18.827 r_dihedral_angle_3_deg 12.25 r_rigid_bond_restr 8.779 r_angle_refined_deg 3.154 r_angle_other_deg 1.874 r_chiral_restr 0.493 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16711 Nucleic Acid Atoms Solvent Atoms 2671 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing