1CP2

NITROGENASE IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1liquid - liquid diffusion7.5PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD. PRECIPITANT CONTAINED 5-15% GLYCEROL, 18.75-22.5% PEG 4000, 230-270 MM CACL2, AND 50 MM HEPES PH 7.5. PROTEIN WAS STORED BEFORE CRYSTALLIZATION IN 20% GLYCEROL, 50 MM HEPES, PH 7.5, AND 2 MM NA2S2O4., liquid - liquid diffusion
Crystal Properties
Matthews coefficientSolvent content
2.1843

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.6α = 90
b = 75.87β = 114.17
c = 53.55γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IIC1993-11-25M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.9315.6398.80.07255.86.83680834.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.93291

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 1NIP1.93531231308398.80.2090.2090.297RANDOM36.3
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24.1
x_angle_deg2
x_improper_angle_d1.89
x_bond_d0.018
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24.1
x_angle_deg2
x_improper_angle_d1.89
x_bond_d0.018
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
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3940
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms8

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
REFSTATdata scaling
X-PLORphasing