4M07

Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145F


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.532980.78 M Ammonium citrate dibasic, 0.1 M Na acetate, 2:1, hanging, pH 4.53, vapor diffusion, temperature 298K, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
2.9658.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.29α = 90
b = 112.61β = 118.49
c = 120.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8726ESRFID23-1

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
12.543.5587.290.0624312.6434897552.93
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)
12.52.5893.0330.231.92676

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.543.551.1848932175983.120.20680.2050.2535Random94.3173
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
f_dihedral_angle_d13.804
f_angle_d1.101
f_chiral_restr0.042
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9524
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms291

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing