6N4L

Dithionite-reduced ADP-bound 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 DROP7.529840% PEG 400, 0.17 mM Cymal 7, 0.1 M HEPES pH 7.5, 5 mM dithionite
Crystal Properties
Matthews coefficientSolvent content
2.0841.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.587α = 90
b = 74.63β = 90
c = 75.398γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.8856SSRLBL12-2

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
11.1353.0411000.0680.0710.0217.612.996897
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)
11.131.1999.90.7990.7990.8350.239111.9

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 REPLACEMENTTHROUGHOUT1G5P1.1339.0492016477099.930.14640.14590.157RANDOM16.113
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]
-0.240.26-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.199
r_dihedral_angle_4_deg16.939
r_sphericity_free14.403
r_dihedral_angle_3_deg12.483
r_sphericity_bonded6.865
r_dihedral_angle_1_deg6.318
r_angle_refined_deg1.466
r_angle_other_deg1.389
r_rigid_bond_restr0.822
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.199
r_dihedral_angle_4_deg16.939
r_sphericity_free14.403
r_dihedral_angle_3_deg12.483
r_sphericity_bonded6.865
r_dihedral_angle_1_deg6.318
r_angle_refined_deg1.466
r_angle_other_deg1.389
r_rigid_bond_restr0.822
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2140
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing