3D78
Dimeric crystal structure of a pheromone binding protein mutant D35N, from apis mellifera, at pH 7.0
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 2.1M ammonium sulfate, 0.2M di ammonium phosphate, 20mM di sodium phosphate, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.054 | α = 90 |
b = 60.948 | β = 90 |
c = 57.334 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | Tiroidal mirror | 2008-02-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.984 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.55 | 50 | 99.6 | 0.048 | 0.048 | 20.3 | 4.4 | 32103 | 32103 | 18.48 |
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) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.55 | 1.63 | 99.6 | 0.321 | 0.321 | 3.8 | 4.2 | 4588 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 3D73 | 1.6 | 15 | 28039 | 28039 | 1200 | 99.54 | 0.16088 | 0.16088 | 0.15897 | 0.20597 | RANDOM | 21.421 |
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] | |
1.17 | -2.08 | 0.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.605 |
r_dihedral_angle_4_deg | 14.447 |
r_dihedral_angle_3_deg | 11.01 |
r_dihedral_angle_1_deg | 10.304 |
r_sphericity_free | 6.128 |
r_scangle_it | 3.187 |
r_scbond_it | 2.546 |
r_sphericity_bonded | 2.272 |
r_mcangle_it | 1.562 |
r_angle_refined_deg | 1.498 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1905 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |