4NYR
In-vivo crystallisation (midguts of a viviparous cockroach) and structure at 2.5 A resolution of a glycosylated, lipid-binding, lipocalin-like protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | In-vivo crystallization | 6 | 300 | Spontaneous crystallization inside the midguts of a living viviparous cockroach, pH 6.0, In-vivo crystallization, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.28 | α = 99.5 |
b = 33.22 | β = 100.28 |
c = 40.18 | γ = 104.11 |
Symmetry | |
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Space Group | P 1 |
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 | 70 | PIXEL | DECTRIS PILATUS 2M-F | 2013-05-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 2.7 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.49 | 50 | 99.6 | 38.07 | 20 | 5421 | 5421 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.49 | 2.56 | 96.7 | 22.43 | 820 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 2.49 | 38.58 | 4876 | 546 | 99.83 | 0.16159 | 0.16159 | 0.15368 | 0.23262 | RANDOM | 17.473 |
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] | |
-0.25 | 0.17 | -0.05 | -0.22 | 0.38 | 0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.737 |
r_dihedral_angle_4_deg | 21.681 |
r_dihedral_angle_3_deg | 18.433 |
r_dihedral_angle_1_deg | 7.515 |
r_long_range_B_refined | 5.678 |
r_mcangle_it | 2.031 |
r_angle_refined_deg | 1.906 |
r_scbond_it | 1.836 |
r_mcbond_it | 1.181 |
r_chiral_restr | 0.122 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1248 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 76 |
Software
Software | |
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Software Name | Purpose |
SOLVE | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |