6BBD
Structure of N-glycosylated porcine surfactant protein-D complexed with glycerol
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU RU300 |
Temperature [K] | 90 |
Detector technology | IMAGE PLATE |
Collection date | 2012-09-05 |
Detector | RIGAKU RAXIS IV++ |
Wavelength(s) | 1.5418 |
Spacegroup name | P 63 |
Unit cell lengths | 66.798, 66.798, 64.974 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 14.852 - 1.898 |
R-factor | 0.2053 |
Rwork | 0.201 |
R-free | 0.24680 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4dn8 |
RMSD bond length | 0.014 |
RMSD bond angle | 1.085 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | PHENIX |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 15.000 | 15.000 | 1.970 |
High resolution limit [Å] | 1.900 | 4.070 | 1.900 |
Rmerge | 0.058 | 0.034 | 0.356 |
Total number of observations | 58032 | ||
Number of reflections | 12304 | 1232 | 871 |
<I/σ(I)> | 23.2 | ||
Completeness [%] | 94.0 | 91.7 | 67.4 |
Redundancy | 4.7 | 5.4 | 2.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | Crystallized in hanging drops by mixing 5 ul protein with 5 ul reservoir solution (0.1 M 2-[bis(2-hydroxyethyl)-amino]-2-(hydroxymethyl)propane-1,3-diol, pH 6.5, 0.2 M MgCl2, 15% glycerol, and 22%-20% PEG 3350) |