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Nickel-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.25 293 18% PEG 8000, 100 mM Tris pH 8.25, 500 mM NaCl, 10 mM dithionite
Crystal Properties Matthews coefficient Solvent content 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.259 α = 90 b = 129.009 β = 109.22 c = 107.76 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 100 PIXEL DECTRIS PILATUS3 S 6M 2018-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.48484, 1.50832 ALS 8.3.1
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 1.99 79.89 99.8 0.939 3.4 5.6 136546 30.36
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 1.99 2.02 99.9 0.003 0.5 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2MIN 1.99 79.89 1.33 135397 6796 98.99 0.2049 0.2023 0.2053 0.2529 0.2561
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.17 f_angle_d 1.793 f_chiral_restr 0.102 f_bond_d 0.019 f_plane_restr 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15657 Nucleic Acid Atoms Solvent Atoms 1009 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction pointless data scaling PHENIX phasing