3NN1

Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with imidazole


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52951.4M sodium/potassium phosphate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0459.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.67α = 90
b = 145.67β = 90
c = 136.44γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.8512697276446268021
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.990.7

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 MODEL1.8547.68134596134596711799.70.181480.181480.179980.20988RANDOM32.5
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]
-0.39-0.19-0.390.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.047
r_dihedral_angle_4_deg19.327
r_dihedral_angle_3_deg14.412
r_dihedral_angle_1_deg5.89
r_scangle_it3.023
r_angle_other_deg2.187
r_scbond_it1.986
r_angle_refined_deg1.399
r_mcangle_it1.255
r_mcbond_it0.721
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.047
r_dihedral_angle_4_deg19.327
r_dihedral_angle_3_deg14.412
r_dihedral_angle_1_deg5.89
r_scangle_it3.023
r_angle_other_deg2.187
r_scbond_it1.986
r_angle_refined_deg1.399
r_mcangle_it1.255
r_mcbond_it0.721
r_mcbond_other0.118
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9595
Nucleic Acid Atoms
Solvent Atoms913
Heterogen Atoms351

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling