5KSI

Crystal structure of deoxygenated hemoglobin in complex with sphingosine phosphate and 2,3-Bisphosphoglycerate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DN2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION6.52980.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5 and 30% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.4750.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.94α = 90
b = 98.08β = 90
c = 65.14γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODECu FINE FOCUS1.54

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
11.83093.90.07611.54.15412419.9
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)
11.81.8696.40.383.43.87

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2DN21.83054123276493.80.18010.2222.7998
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]
1.667-4.4652.798
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.76
c_scbond_it1.987
c_mcangle_it1.602
c_mcbond_it1.199
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4384
Nucleic Acid Atoms
Solvent Atoms784
Heterogen Atoms286

Software

Software
Software NamePurpose
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing