2E56
Crystal structure of human MD-2
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.3 | 277 | 20% PEG8000, 120mM Na-acetate,70mM Na-cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.113 | α = 90 |
b = 53.113 | β = 90 |
c = 111.447 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | CCD | RIGAKU JUPITER 210 | 2006-10-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.0000 | SPring-8 | BL38B1 |
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 | 2 | 48.4 | 99.5 | 0.105 | 11.3 | 12.3 | 11389 | 26.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MIR | THROUGHOUT | 2 | 48.39 | 3 | 9641 | 477 | 88.74 | 0.19648 | 0.19407 | 0.24922 | RANDOM | 39.557 |
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] | |
0.81 | 0.81 | -1.61 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.988 |
r_dihedral_angle_3_deg | 15.402 |
r_dihedral_angle_4_deg | 14.207 |
r_scangle_it | 7.736 |
r_dihedral_angle_1_deg | 6.146 |
r_mcangle_it | 5.947 |
r_scbond_it | 5.345 |
r_mcbond_it | 4.099 |
r_angle_refined_deg | 1.543 |
r_nbtor_refined | 0.338 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1162 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 76 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHARP | phasing |