3NN4

Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN-HOUSE MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42950.4-0.6M ammonium sulphate, 0.1M citric acid, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0259.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.41α = 90
b = 113.88β = 118.02
c = 119.87γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.933ESRFID14-1

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
12.710691.544825
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.7780.9

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN-HOUSE MODEL2.743.724251042510225699.840.218310.218310.216090.25798RANDOM77.041
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]
-0.3-8.42-2.13-5.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.342
r_dihedral_angle_4_deg19.801
r_dihedral_angle_3_deg18.062
r_dihedral_angle_1_deg5.568
r_scangle_it1.694
r_angle_refined_deg1.325
r_scbond_it1.162
r_angle_other_deg0.909
r_mcangle_it0.574
r_mcbond_it0.457
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.342
r_dihedral_angle_4_deg19.801
r_dihedral_angle_3_deg18.062
r_dihedral_angle_1_deg5.568
r_scangle_it1.694
r_angle_refined_deg1.325
r_scbond_it1.162
r_angle_other_deg0.909
r_mcangle_it0.574
r_mcbond_it0.457
r_symmetry_hbond_refined0.4
r_symmetry_vdw_refined0.254
r_symmetry_vdw_other0.253
r_nbd_refined0.211
r_mcbond_other0.21
r_nbd_other0.191
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.175
r_xyhbond_nbd_other0.144
r_nbtor_other0.086
r_chiral_restr0.071
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9585
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms320

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling