7ADR

CO bound as bridging ligand at the active site of vanadium nitrogenase VFe protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FEA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Tris/HCl pH 7.5, magnesium chloride, ethylene glycol, PEG 8000, sodium dithionite
Crystal Properties
Matthews coefficientSolvent content
2.4850.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.579α = 84.11
b = 79.934β = 72.42
c = 107.223γ = 75.19
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.849205SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
1148.4588.10.99810.67.61101498
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.020.592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6FEA148.451095802564988.130.10190.10190.1169RANDOM14.169
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]
0.270.220.550.69-0.17-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.599
r_dihedral_angle_1_deg20.256
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg12.25
r_rigid_bond_restr8.779
r_angle_refined_deg3.154
r_angle_other_deg1.874
r_chiral_restr0.493
r_bond_refined_d0.023
r_gen_planes_refined0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.599
r_dihedral_angle_1_deg20.256
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg12.25
r_rigid_bond_restr8.779
r_angle_refined_deg3.154
r_angle_other_deg1.874
r_chiral_restr0.493
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16711
Nucleic Acid Atoms
Solvent Atoms2671
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing