6VXT

Activated 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, 0.16 M ammonium acetate, 0.1 M sodium citrate(pH 5.0), 25.6 % v/v glycerol, 5 mM sodium dithionite
Crystal Properties
Matthews coefficientSolvent content
2.9558.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.535α = 90
b = 203.435β = 103.945
c = 83.857γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-12-17MSINGLE 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
11.735096.80.150.060.98917.46.126363432.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.7671.90.970.3224

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 3U7Q1.7441.711.34262041198396.10.17260.17240.202944.19
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_d9.284
f_angle_d0.8507
f_chiral_restr0.0528
f_bond_d0.007
f_plane_restr0.0055
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15617
Nucleic Acid Atoms
Solvent Atoms1234
Heterogen Atoms148

Software

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