1M1N

Nitrogenase MoFe protein from Azotobacter vinelandii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MINPDB entry 3MIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8298PEG 8000, sodium chloride, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.31α = 90
b = 131.63β = 108.37
c = 159.159γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152002-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.992SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.1610095.60.090.078102.5145451913905201112.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.161.18900.5350.5541.62.565290

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 3MIN1.1650145451913767241373395.610.123490.123230.14924RANDOM15.839
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]
0.261.13-0.430.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.902
r_sphericity_free9.996
r_sphericity_bonded6.275
r_dihedral_angle_1_deg5.831
r_scangle_it5.698
r_scbond_it4.054
r_mcangle_it2.894
r_rigid_bond_restr2.613
r_mcbond_it2.258
r_angle_refined_deg2.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.902
r_sphericity_free9.996
r_sphericity_bonded6.275
r_dihedral_angle_1_deg5.831
r_scangle_it5.698
r_scbond_it4.054
r_mcangle_it2.894
r_rigid_bond_restr2.613
r_mcbond_it2.258
r_angle_refined_deg2.251
r_nbtor_other1.049
r_angle_other_deg1.039
r_symmetry_hbond_refined0.828
r_symmetry_vdw_refined0.396
r_xyhbond_nbd_other0.382
r_symmetry_vdw_other0.373
r_nbd_refined0.333
r_nbd_other0.263
r_xyhbond_nbd_refined0.225
r_chiral_restr0.163
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms32171
Nucleic Acid Atoms
Solvent Atoms5021
Heterogen Atoms192

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling