5KOH | pdb_00005koh

Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529345% 2-methyl-2,4-pentadiol (MPD) , 300 mM NaCl, 100 mM Na Cacodylate, pH 6.5, 1 mM Spermine, 0.1% Zwittergent, and 5 mM Na2S2O4
Crystal Properties
Matthews coefficientSolvent content
359.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 202.598α = 90
b = 202.598β = 90
c = 132.567γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELDECTRIS PILATUS 6M2016-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.98SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)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
11.83143.261000.42080.42880.97612.8527.224020014.27
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.8951001.4340.8151.4627.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1M1N1.83143.262282281194399.970.129720.128640.14210.150390.1625RANDOM17.981
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]
-0.37-0.370.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.23
r_dihedral_angle_4_deg18.405
r_dihedral_angle_3_deg13.226
r_long_range_B_refined6.714
r_long_range_B_other6.235
r_dihedral_angle_1_deg6.132
r_scangle_other4.705
r_scbond_it3.091
r_scbond_other3.091
r_angle_refined_deg2.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.23
r_dihedral_angle_4_deg18.405
r_dihedral_angle_3_deg13.226
r_long_range_B_refined6.714
r_long_range_B_other6.235
r_dihedral_angle_1_deg6.132
r_scangle_other4.705
r_scbond_it3.091
r_scbond_other3.091
r_angle_refined_deg2.015
r_mcangle_it2.014
r_mcangle_other2.014
r_angle_other_deg1.79
r_mcbond_it1.455
r_mcbond_other1.455
r_chiral_restr0.148
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15640
Nucleic Acid Atoms
Solvent Atoms1979
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata scaling
Aimlessdata scaling
PHASERphasing