5OXS

Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PW9pdbid 1PW9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Tris pH 8.0, 16% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
358.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.679α = 90
b = 108.51β = 92.89
c = 56.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.6556.1930.0540.0650.0360.99811.43.174199
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6893.20.3970.480.2660.6943

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdbid 1PW91.6556.170522364792.840.16580.16470.1868RANDOM23.384
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]
0.290.050.34-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.538
r_dihedral_angle_3_deg10.956
r_dihedral_angle_4_deg8.401
r_dihedral_angle_1_deg5.321
r_angle_refined_deg1.324
r_angle_other_deg0.914
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.538
r_dihedral_angle_3_deg10.956
r_dihedral_angle_4_deg8.401
r_dihedral_angle_1_deg5.321
r_angle_refined_deg1.324
r_angle_other_deg0.914
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3499
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms161

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction