6RKZ

Recombinant Pseudomonas stutzeri nitrous oxide reductase, form II


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M bis-tris propane buffer at pH 8.5, 0.1 M sodium formate, 0.1 M sodium chloride, and 25% (w/v) of a medium molecular weight (MMW) polyethylene glycol mixture (PEG 2K, 3350, 4K and 5K MME)
Crystal Properties
Matthews coefficientSolvent content
238.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.887α = 90
b = 76.789β = 93.33
c = 108.823γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2018-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.36999SLSX06DA

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
11.676.7992.2147190846
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.79

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3SBQ1.60159.6961.94190846955865.070.15390.15180.1911
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_d13.267
f_angle_d1.097
f_chiral_restr0.068
f_bond_d0.01
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9221
Nucleic Acid Atoms
Solvent Atoms921
Heterogen Atoms88

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing