4DN8
Structure of porcine surfactant protein D neck and carbohydrate recognition domain complexed with mannose
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU RU300 |
Temperature [K] | 100 |
Detector technology | IMAGE PLATE |
Collection date | 2010-10-25 |
Detector | RIGAKU RAXIS IV |
Wavelength(s) | 1.5418 |
Spacegroup name | P 63 |
Unit cell lengths | 66.024, 66.024, 66.018 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 14.763 - 2.200 |
R-factor | 0.2028 |
Rwork | 0.199 |
R-free | 0.23730 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | A complex of pig SPD and glycerol solved by molecular replacement in the same space group using human SPD (pdb code 2GGU B chain) |
RMSD bond length | 0.002 |
RMSD bond angle | 0.542 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | PHASER |
Refinement software | PHENIX ((phenix.refine: 1.6.3_473)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 15.000 | 2.280 |
High resolution limit [Å] | 2.200 | 2.200 |
Rmerge | 0.044 | 0.418 |
Number of reflections | 8327 | |
<I/σ(I)> | 33.9 | 7.25 |
Completeness [%] | 99.5 | 99.3 |
Redundancy | 10.8 | 9.4 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 290 | 12.3 mg/ml protein in 0.9 % sodium chloride, 5 mM EDTA, 15 mM calcium chloride, and 20 mM mannose was mixed with an equal volume of 0.1 M bistris (pH =6.5), 20% w/v PEG 3350, 200 mM magesium chloride, and 15% v/v glycerol. Prior to data collection crystals were soaked in a 30% w/v D-mannose solution., VAPOR DIFFUSION, HANGING DROP, temperature 290K |