5N6Y

Azotobacter vinelandii vanadium nitrogenase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529310-13 % (w/v) of polyethylene glycol 8000 15-20 % (v/v) of ethylene glycol 0.03 M MgCl2 0.1 mM ZnCl2 5 mM Na2S2O4 0.1 M of HEPES/NaOH pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4850.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.25α = 84.06
b = 79.79β = 72.62
c = 106.97γ = 75.15
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.35102.0496.10.0620.0470.99810.43.546059322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3992.31.0480.780.4943.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.35102.044605932384696.10.110640.108810.14595RANDOM18.371
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]
-0.030.08-0.31-0.330.070.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.401
r_sphericity_free24.472
r_dihedral_angle_4_deg19.109
r_dihedral_angle_3_deg12.97
r_sphericity_bonded10.072
r_dihedral_angle_1_deg6.028
r_rigid_bond_restr5.943
r_scangle_other4.327
r_long_range_B_refined4.193
r_angle_refined_deg4.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.401
r_sphericity_free24.472
r_dihedral_angle_4_deg19.109
r_dihedral_angle_3_deg12.97
r_sphericity_bonded10.072
r_dihedral_angle_1_deg6.028
r_rigid_bond_restr5.943
r_scangle_other4.327
r_long_range_B_refined4.193
r_angle_refined_deg4.057
r_scbond_other3.904
r_scbond_it3.903
r_long_range_B_other3.89
r_mcangle_it2.454
r_mcangle_other2.454
r_mcbond_it2.287
r_mcbond_other2.285
r_angle_other_deg1.68
r_chiral_restr0.298
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16680
Nucleic Acid Atoms
Solvent Atoms2249
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing