5NGH
Structure of Odorant Binding Protein 3 from Giant Panda (Ailuropoda melanoleuca)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 273 | 2.2 M Ammonium Sulfate and 0.2M Potassium Nitrate at pH 7.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.71 | 66.89 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 94.03 | α = 90 |
b = 94.03 | β = 90 |
c = 114.53 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2016-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.97 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.8 | 80 | 99.9 | 0.2 | 0.998 | 10.4 | 10.4 | 7821 | 104.93 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.8 | 2.97 | 99.8 | 0.93 | 10.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3KFF | 2.8 | 24.73 | 7784 | 389 | 99.65 | 0.2772 | 0.2766 | 0.2877 | RANDOM | 93.18 |
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] | |
-27.4321 | -27.4321 | 54.8641 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 25.38 |
t_omega_torsion | 2.93 |
t_angle_deg | 1.26 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1272 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 16 |
Software
Software | |
---|---|
Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |