2ORK

crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with inositol-1-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GGUPDB entry 2GGU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5290150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.2161.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.403α = 90
b = 108.01β = 91.83
c = 55.701γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.0NSLSX8C

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
11.938.6692.70.0380.03846.23.85191748123
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)
1.91.9772.60.0670.0671723737

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2GGU1.8938.664777644155390092.420.189640.189640.186420.22611RANDOM21.249
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]
0.070.320.15-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.579
r_dihedral_angle_4_deg13.889
r_dihedral_angle_3_deg12.862
r_dihedral_angle_1_deg5.477
r_scangle_it3.659
r_scbond_it2.284
r_mcangle_it1.385
r_angle_refined_deg1.247
r_mcbond_it1.082
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.579
r_dihedral_angle_4_deg13.889
r_dihedral_angle_3_deg12.862
r_dihedral_angle_1_deg5.477
r_scangle_it3.659
r_scbond_it2.284
r_mcangle_it1.385
r_angle_refined_deg1.247
r_mcbond_it1.082
r_nbtor_refined0.3
r_nbd_refined0.205
r_symmetry_vdw_refined0.199
r_symmetry_hbond_refined0.165
r_metal_ion_refined0.164
r_xyhbond_nbd_refined0.142
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3457
Nucleic Acid Atoms
Solvent Atoms517
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing