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Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN, with Av1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6N4L PDB entry 6N4L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7
Crystal Properties Matthews coefficient Solvent content 2.02 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.835 α = 90 b = 74.406 β = 90 c = 74.689 γ = 90
Symmetry Space Group P 2 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 PILATUS 6M 2020-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97239, 0.98062 SSRL BL12-2
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 1.6 45.85 99.5 0.055 0.064 0.034 0.999 14.1 6.6 34297 20.18
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 1.6 1.63 97.1 0.902 1.07 0.568 0.851 6.5
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 THROUGHOUT PDB entry 6N4L 1.6 39.02 1.33 34134 3147 99.03 0.1723 0.1712 0.1731 0.1942 0.1936 27.6176
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2057 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 36
Software Software Software Name Purpose Aimless data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction