1OEE

YodA from Escherichia coli crystallised with cadmium ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherZN CRYSTAL FORM OF YODA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.510 MG/ML PROTEIN, 10% PEG 10000, 100 MM SODIUM CACODYLATE, PH = 6.5 20 MM CADMIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.346.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.47α = 90
b = 47.985β = 92.77
c = 42.493γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMULTILAYER MIRROR2001-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLURE BEAMLINE DW32LUREDW32

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
12.134.0693.80.07214.353.11231720.107
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)
12.12.1864.90.3083.21.8

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 REPLACEMENTTHROUGHOUTZN CRYSTAL FORM OF YODA2.153.451171558896.170.17090.1690.208RANDOM20.692
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]
0.04-0.281.1-1.16
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1513
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4phasing
REFMACrefinement