2ZON

Crystal structure of electron transfer complex of nitrite reductase with cytochrome c


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OE1PDB ENTRY 1oe1, 1kx7
experimental modelPDB 1KX7PDB ENTRY 1oe1, 1kx7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.4277PEG 3350, Magnesium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2745.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.345α = 90
b = 103.942β = 90
c = 163.144γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402007-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.743.898.8119863119863
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7697.7

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 1oe1, 1kx71.781053321172798.780.165480.162170.19542RANDOM18.525
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]
-0.741-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.604
r_dihedral_angle_4_deg20.154
r_dihedral_angle_3_deg13.887
r_dihedral_angle_1_deg11.835
r_scangle_it3.188
r_scbond_it2.007
r_angle_refined_deg1.496
r_mcangle_it1.139
r_mcbond_it0.762
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.604
r_dihedral_angle_4_deg20.154
r_dihedral_angle_3_deg13.887
r_dihedral_angle_1_deg11.835
r_scangle_it3.188
r_scbond_it2.007
r_angle_refined_deg1.496
r_mcangle_it1.139
r_mcbond_it0.762
r_nbtor_refined0.306
r_symmetry_vdw_refined0.229
r_nbd_refined0.201
r_chiral_restr0.118
r_xyhbond_nbd_refined0.116
r_symmetry_hbond_refined0.112
r_metal_ion_refined0.022
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8242
Nucleic Acid Atoms
Solvent Atoms1073
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling