3FLT

Crystal structure of PE-bound octameric SAP-like pentraxin from Limulus polyphemus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FLRCrystals were isomorphous to octameric native. Native structure, pdb code 3FLR, was used in rigid body refinement.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7298PEG 6000, CaCl2, MES, PE, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.8467.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.39α = 90
b = 172.39β = 90
c = 98.37γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-04-03SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.488SRSPX14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.760.68199.60.0840.0844.9753.82053020530
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.8598.90.2520.2522.63.92928

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTCrystals were isomorphous to octameric native. Native structure, pdb code 3FLR, was used in rigid body refinement.2.760.682052920529104099.40.2430.2430.210.243Random28.337
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]
1.2711.271-2.542
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.839
c_mcangle_it1.969
c_scbond_it1.908
c_mcbond_it1.154
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3336
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms22

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction