5BVG

Selenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A. vinelandii


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 8000, NaCl, Imidazole/Malate, Sodiumdithionite
Crystal Properties
Matthews coefficientSolvent content
2.2445.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.582α = 90
b = 130.825β = 108.85
c = 107.128γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97918SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.638.7697.80.1519.57.1256394
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6997.80.7952.37.1

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 REPLACEMENTTHROUGHOUT3U7Q1.6101.382436571269196.560.152920.151560.17913RANDOM13.776
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]
0.660.37-0.53-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.584
r_sphericity_free20.813
r_dihedral_angle_4_deg19.58
r_dihedral_angle_3_deg12.519
r_dihedral_angle_1_deg5.969
r_sphericity_bonded3.236
r_long_range_B_refined1.781
r_long_range_B_other1.781
r_angle_refined_deg1.53
r_angle_other_deg1.484
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.584
r_sphericity_free20.813
r_dihedral_angle_4_deg19.58
r_dihedral_angle_3_deg12.519
r_dihedral_angle_1_deg5.969
r_sphericity_bonded3.236
r_long_range_B_refined1.781
r_long_range_B_other1.781
r_angle_refined_deg1.53
r_angle_other_deg1.484
r_scangle_other0.82
r_rigid_bond_restr0.711
r_mcangle_it0.696
r_mcangle_other0.696
r_scbond_it0.665
r_scbond_other0.665
r_mcbond_it0.536
r_mcbond_other0.536
r_chiral_restr0.094
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms15897
Nucleic Acid Atoms
Solvent Atoms1433
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
Cootmodel building
XDSdata scaling
XDSdata reduction
MOLREPphasing