5KSJ

Crystal structure of deoxygenated hemoglobin in complex with Sphingosine phosphate


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
2.4349.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.18α = 90
b = 97.55β = 90
c = 65.03γ = 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
12.43096.60.129.45.0824236
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)
12.42.4996.80.3983.14.13

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 REPLACEMENT2DN22.43024093122799.10.22170.287243.7645
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]
-6.625-10.21316.838
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it7.181
c_scbond_it5.758
c_mcangle_it5.633
c_mcbond_it3.967
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4384
Nucleic Acid Atoms
Solvent Atoms545
Heterogen Atoms208

Software

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