6N4K

Dithionite-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 DROP6.5298of 40% PEG 1000, 0.2 M NaCl, 0.1 M MES/OH pH 6.5, 10% 2,2,2-trifluoroethanol, 5 mM dithionite
Crystal Properties
Matthews coefficientSolvent content
2.1442.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.62α = 90
b = 45.199β = 96.58
c = 108.772γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.0SSRLBL12-2

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
11.756108.05596.50.0450.0490.019226.748484
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)
11.7561.8581.80.2080.2080.2280.0923.65.7

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 REPLACEMENTTHROUGHOUT1G5P1.75639.2946085236996.180.17290.17080.213RANDOM31.362
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]
0.13-0.840.67-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.72
r_sphericity_free21.645
r_dihedral_angle_4_deg16.111
r_dihedral_angle_3_deg14.427
r_sphericity_bonded12.071
r_dihedral_angle_1_deg6.442
r_angle_refined_deg1.703
r_angle_other_deg1.597
r_rigid_bond_restr1.283
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.72
r_sphericity_free21.645
r_dihedral_angle_4_deg16.111
r_dihedral_angle_3_deg14.427
r_sphericity_bonded12.071
r_dihedral_angle_1_deg6.442
r_angle_refined_deg1.703
r_angle_other_deg1.597
r_rigid_bond_restr1.283
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4093
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction