3PAK

Crystal Structure of Rat Surfactant Protein A neck and carbohydrate recognition domain (NCRD) complexed with Mannose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R13PDB ENTRY 1R13

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52901 ul SP-A (10 mg/ml) was mixed with 1 ul reservoir (50 mM sodium cacodylate (ph = 6.5), 1.2-1.6 M lithium sulfate, and 10 mM calcium chloride). After crystals grew, the drop was diluted 1/2 with 50 mM sodium cacodylate (pH =6.5) and 10 mM calcium chloride. Then, mannose powder was added to the drop and mixed to dissolve. A second dilution by 1/2 again and addition of more mannose powder preceded data collection., VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.7367.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.796α = 90
b = 97.796β = 90
c = 45.088γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90IMAGE PLATERIGAKU RAXIS IV2006-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.95099.40.0524.5519500-327.3
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)
1.91.9498.90.2874.53.91279

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1R131.926.119155150797.70.2180.2180.243RANDOM36.9
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]
4.352.624.35-8.7
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_angle_deg1.1
c_improper_angle_d0.69
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_angle_deg1.1
c_improper_angle_d0.69
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1143
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms19

Software

Software
Software NamePurpose
CrystalCleardata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing