6N4J

Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G5P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529837% PEG 3350, 0.05 M NaCl, 0.1 M Bis/Tris pH 5.5, 5 mM Ti(III) citrate
Crystal Properties
Matthews coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.25α = 90
b = 93.05β = 98.5
c = 60.77γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9801SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.9560.10290.70.0590.0640.02611.25.441566
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0692.40.4460.4460.4950.2111.55.2

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 REPLACEMENTTHROUGHOUT1G5P1.9544.6839130198789.690.21590.21410.249RANDOM48.932
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]
-1.712.74-5.135.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.125
r_dihedral_angle_4_deg20.526
r_dihedral_angle_3_deg15.766
r_dihedral_angle_1_deg6.824
r_angle_refined_deg2.268
r_angle_other_deg1.622
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.125
r_dihedral_angle_4_deg20.526
r_dihedral_angle_3_deg15.766
r_dihedral_angle_1_deg6.824
r_angle_refined_deg2.268
r_angle_other_deg1.622
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4280
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction