4XPI

Fe protein independent substrate reduction by nitrogenase variants altered in intramolecular electron transfer


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION829830% PEG 4000, 100mM Tris-HCl pH 8.0, 170-190mM Sodium molybdate and 1mM Dithionite, LIQUID DIFFUSION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2946.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.804α = 90
b = 130.83β = 111.14
c = 108.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2012-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9735.896.392.53.5141514

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 REPLACEMENTTHROUGHOUT3U7Q1.9735134339708796.390.215570.213030.26359RANDOM41.796
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]
3.660.5-0.91-2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.531
r_dihedral_angle_4_deg21.525
r_dihedral_angle_3_deg14.534
r_dihedral_angle_1_deg6.738
r_angle_refined_deg2.922
r_angle_other_deg1.404
r_chiral_restr0.273
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.531
r_dihedral_angle_4_deg21.525
r_dihedral_angle_3_deg14.534
r_dihedral_angle_1_deg6.738
r_angle_refined_deg2.922
r_angle_other_deg1.404
r_chiral_restr0.273
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15937
Nucleic Acid Atoms
Solvent Atoms921
Heterogen Atoms202

Software

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