2ORJ

crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with N-acetyl mannosamine


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
3.2562.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.63α = 90
b = 108.33β = 91.51
c = 55.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-08-01MSINGLE 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
11.826.5980.0450.04525.83.86134560089
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)
1.81.8696.20.170.179.73.55874

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 2GGU1.826.475627054297484496.510.180590.180590.17840.20545RANDOM23.32
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]
0.09-0.330.97-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.15
r_dihedral_angle_4_deg18.938
r_dihedral_angle_3_deg12.899
r_dihedral_angle_1_deg5.128
r_scangle_it3.514
r_scbond_it2.175
r_mcangle_it1.33
r_angle_refined_deg1.246
r_mcbond_it1.053
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.15
r_dihedral_angle_4_deg18.938
r_dihedral_angle_3_deg12.899
r_dihedral_angle_1_deg5.128
r_scangle_it3.514
r_scbond_it2.175
r_mcangle_it1.33
r_angle_refined_deg1.246
r_mcbond_it1.053
r_nbtor_refined0.3
r_symmetry_vdw_refined0.207
r_nbd_refined0.204
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.12
r_metal_ion_refined0.081
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3462
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms54

Software

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