3M4B
A Zn-mediated tetrahedral protein lattice cage
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 25% PEG 1500, 0.1 M Bis-Tris, 0.2 M CaCl2 and 5 mM ZnCl2., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.94 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 125.363 | ¦Á = 90 |
b = 125.363 | ¦Â = 90 |
c = 164.509 | ¦Ã = 120 |
Symmetry | |
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Space Group | H 3 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 | MARMOSAIC 325 mm CCD | Flat collimating mirror, double crystal monochromator, toroid focusing mirror | 2009-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 1.18 | SSRL | BL9-2 |
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 | 2.5 | 90.614 | 100 | 0.106 | 0.106 | 16.5 | 6 | 17431 | 17431 |
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) | ||||||||||
2.5 | 2.64 | 100 | 0.481 | 0.481 | 1.5 | 5.4 | 2495 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | THROUGHOUT | 2.5 | 41.27 | 16174 | 1257 | 99.98 | 0.20206 | 0.19791 | 0.25558 | RANDOM | 34.565 |
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] | |
-0.21 | -0.1 | -0.21 | 0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.975 |
r_dihedral_angle_4_deg | 19.206 |
r_dihedral_angle_3_deg | 17.655 |
r_dihedral_angle_1_deg | 4.742 |
r_scangle_it | 2.379 |
r_scbond_it | 1.546 |
r_angle_refined_deg | 1.301 |
r_mcangle_it | 0.889 |
r_mcbond_it | 0.521 |
r_nbtor_refined | 0.283 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3256 |
Nucleic Acid Atoms | |
Solvent Atoms | 81 |
Heterogen Atoms | 200 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
MOSFLM | data reduction |
MOLREP | phasing |