3VM0

Assimilatory nitrite reductase (Nii3) - N226K mutant - NO2 complex from tobacco leaf


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B0G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5277PEG4000, Tris-HCl, MgCl2, MPD, NaNO2, pH 8.5, vapor diffusion, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6353.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.229α = 90
b = 133.229β = 90
c = 77.644γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210rRh coated collimating and focusing Si mirror2010-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.6955098.40.06311.612761657616526.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6951.7694.70.5065.2411.17216

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 REPLACEMENTTHROUGHOUT3B0G1.69526.76759777597738191000.16420.1630.1857RANDOM21.0945
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]
0.380.38-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.479
r_dihedral_angle_4_deg12.431
r_dihedral_angle_3_deg12.277
r_dihedral_angle_1_deg6.021
r_scangle_it3.385
r_scbond_it2.075
r_angle_refined_deg1.297
r_mcangle_it1.169
r_mcbond_it0.617
r_metal_ion_refined0.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.479
r_dihedral_angle_4_deg12.431
r_dihedral_angle_3_deg12.277
r_dihedral_angle_1_deg6.021
r_scangle_it3.385
r_scbond_it2.075
r_angle_refined_deg1.297
r_mcangle_it1.169
r_mcbond_it0.617
r_metal_ion_refined0.373
r_nbtor_refined0.305
r_symmetry_hbond_refined0.219
r_nbd_refined0.207
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.152
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4248
Nucleic Acid Atoms
Solvent Atoms758
Heterogen Atoms77

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction