6OP1

Selenium incorporated, carbon monoxide inhibited FeMo-cofactor of azotobacter vinelandii


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829126% 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
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.191α = 90
b = 128.003β = 109.15
c = 107.633γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9791SSRLBL12-2

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
11.736.9398.60.1150.1240.0460.997116.9213040
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)
11.71.7398.80.5710.6180.2330.8676.9

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 REPLACEMENTTHROUGHOUT3u7q1.736.932025911047998.480.13380.13220.1648RANDOM15.479
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_deg34.938
r_dihedral_angle_4_deg21.219
r_dihedral_angle_3_deg13.195
r_dihedral_angle_1_deg6.463
r_angle_refined_deg1.766
r_angle_other_deg1.073
r_chiral_restr1.047
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.938
r_dihedral_angle_4_deg21.219
r_dihedral_angle_3_deg13.195
r_dihedral_angle_1_deg6.463
r_angle_refined_deg1.766
r_angle_other_deg1.073
r_chiral_restr1.047
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15869
Nucleic Acid Atoms
Solvent Atoms1771
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing