6OP3

Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low concentration of selenium


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29126% v/v PEG6000, 0.75 M sodium chloride, 12.5% v/v MPD, 0.1 M imidazole/malate buffer, pH 8.0, 5 mM Na2S2O4
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.872α = 90
b = 131.023β = 110.62
c = 106.957γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.979SSRLBL12-2

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
11.637.8598.70.0570.0680.0360.97414.43.4269898
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)
11.61.6398.90.2020.2430.1340.9483.3

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 REPLACEMENTTHROUGHOUT3u7q1.637.852565351341798.610.12810.12690.1522RANDOM13.612
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
r_dihedral_angle_2_deg34.609
r_dihedral_angle_4_deg21.311
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg6.332
r_angle_refined_deg1.92
r_angle_other_deg1.149
r_chiral_restr1.093
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.609
r_dihedral_angle_4_deg21.311
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg6.332
r_angle_refined_deg1.92
r_angle_other_deg1.149
r_chiral_restr1.093
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15878
Nucleic Acid Atoms
Solvent Atoms2150
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing