3U7Q

A. vinelandii nitrogenase MoFe protein at atomic resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M1NPDB ENTRY 1M1N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829116.5% v/v PEG6000, 0.55 M sodium chloride, 12.5% v/v MPD, 1.5% v/v xylitol, 0.2 M imidazole/malate buffer, pH 8.0, 0.1 mM Zwittergent 3-14, 0.55 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3246.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.19α = 90
b = 130.696β = 110.67
c = 107.224γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.8SLSX06SA

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
1147.45799.10.18.66.431122961111285422
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)
111.0998.30.6871.55.55

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1M1N147.457111285410561835590399.160.129320.128440.14603RANDOM8.079
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]
0.30.010.03-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.432
r_dihedral_angle_2_deg36.166
r_dihedral_angle_4_deg20.094
r_dihedral_angle_3_deg11.636
r_sphericity_bonded8.834
r_dihedral_angle_1_deg6.067
r_rigid_bond_restr2.496
r_angle_other_deg1.556
r_angle_refined_deg1.541
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.432
r_dihedral_angle_2_deg36.166
r_dihedral_angle_4_deg20.094
r_dihedral_angle_3_deg11.636
r_sphericity_bonded8.834
r_dihedral_angle_1_deg6.067
r_rigid_bond_restr2.496
r_angle_other_deg1.556
r_angle_refined_deg1.541
r_chiral_restr0.099
r_bond_refined_d0.011
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 Atoms15928
Nucleic Acid Atoms
Solvent Atoms2602
Heterogen Atoms168

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling