6BBE
Structure of N-glycosylated porcine surfactant protein-D
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 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) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.39 | 48.63 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 66.015 | α = 90 |
b = 66.015 | β = 90 |
c = 64.658 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 63 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 90 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2013-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.9 | 15 | 96 | 0.063 | 25.4 | 6.5 | 12220 | 34.17 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.9 | 1.97 | 82.2 | 0.376 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
X-RAY DIFFRACTION | 1.898 | 14.699 | 11637 | 1184 | 91.51 | 0.2259 | 0.2232 | 0.2501 | 47.45 |
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] | |
9.4814 | 9.4814 | -18.9627 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 26.386 |
f_angle_d | 0.805 |
f_chiral_restr | 0.051 |
f_bond_d | 0.013 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1193 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 108 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data collection |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
PHENIX | phasing |