7TQ0

Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN, with Av1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6N4LPDB entry 6N4L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529836-41% 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 coefficientSolvent content
2.0439.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.035α = 90
b = 74.636β = 90
c = 74.88γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97869, 0.98062SSRLBL12-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8145.9499.60.1340.1450.0540.99914.513.12417518.35
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)RedundancyNumber Unique Reflections (All)
11.811.8597.81.9622.1290.8160.79712.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 6N4L1.8137.321.3324110222699.560.18510.18330.219826.7191
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 AtomsNumber
Protein Atoms2057
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms36

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction