2RIC

Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with L-glycero-D-manno-heptopyranosyl-(1-3)-L-glycero-D-manno-heptopyranose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429012% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES , PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.261.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.404α = 90
b = 107.531β = 90.28
c = 55.698γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.85095.30.05720.23.457647
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)
1.81.8468.30.322.32722

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.85056481575293.70.2050.2333.814
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]
0.7181.064-5.384.663
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.925
c_scbond_it1.966
c_mcangle_it1.593
c_mcbond_it1.122
c_angle_deg1.1102
c_bond_d0.0054
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3540
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms77

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing