6UG0

N2-bound Nitrogenase MoFe-protein from Azotobacter vinelandii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U7QPDB entry 3U7Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529314-19 % w/v PEG smear high, 0.16M ammonium acetate, 0.1M sodium citrate (pH 5.0), 25.6 % v/v glycerol, 5mM Eu(II)-EGTA
Crystal Properties
Matthews coefficientSolvent content
2.9257.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.362α = 90
b = 156.967β = 90
c = 202.343γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M22019-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.0000SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.835095.20.2150.0610.99411.511.523728331.55
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.8694.83.1631.0350.3529

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 REPLACEMENTFREE R-VALUEPDB entry 3U7Q1.8339.191.33222639196993.840.2180.21760.258749.87
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d3.9127
f_angle_d0.9927
f_chiral_restr0.054
f_bond_d0.0089
f_plane_restr0.0066
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15576
Nucleic Acid Atoms
Solvent Atoms777
Heterogen Atoms159

Software

Software
Software NamePurpose
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXrefinement