2NIP

NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NIPPDB ENTRY 1NIP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1liquid-liquid diffusion8PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD, USING 25-30% PEG 4000, 140-200 MM NA2MOO4, 100 MM TRIS-CL, PH 8.0; PROTEIN WAS HELD IN A BUFFER OF 20% GLYCEROL, 50 MM TRIS-CL, PH 8.0, 450 MM NACL, AND 2 MM NA2S2O4 PRIOR TO CRYSTALLIZATION., liquid-liquid diffusion
Crystal Properties
Matthews coefficientSolvent content
2.447

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.12α = 90
b = 90.53β = 90
c = 91.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATEMARRESEARCHMIRROR1995-03-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-1SSRLBL7-1

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
12.135092.90.0850.0856.942906035
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)
2.22.2894.90.3090.3092.43.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NIP2.25029180173792.90.2230.2230.29RANDOM31.7
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]
-19.79-4.98-11.26
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.9
x_scangle_it5.18
x_mcangle_it3.64
x_scbond_it3.62
x_mcbond_it2.4
x_angle_deg1.9
x_improper_angle_d1.64
x_bond_d0.017
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.9
x_scangle_it5.18
x_mcangle_it3.64
x_scbond_it3.62
x_mcbond_it2.4
x_angle_deg1.9
x_improper_angle_d1.64
x_bond_d0.017
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4356
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms8

Software

Software
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling