3EG5
Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Z2C | PDB ENTRY 1Z2C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.8 | 293 | Bis-Tris-Propane (PH 8.8 adjusted with citric acid), 26% (w/v) PEG 3350, 250mM Na-Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.15 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 71.269 | ¦Á = 90 |
b = 71.269 | ¦Â = 90 |
c = 244.964 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 |
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 | MAR CCD 165 mm | MIRRORS | 2007-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.9763 | SLS | X10SA |
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 | 2.7 | 43.478 | 99.5 | 0.074 | 0.084 | 13.52 | 3.2 | 38241 | 38038 |
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) | ||||||||||
2.7 | 2.8 | 99.8 | 0.381 | 0.333 | 3.69 | 3.2 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1Z2C | 2.7 | 43.47 | 38038 | 36130 | 1908 | 99.49 | 0.20816 | 0.20629 | 0.24333 | RANDOM | 53.029 |
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] | |
0.19 | 0.09 | 0.19 | -0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.536 |
r_dihedral_angle_3_deg | 17.867 |
r_dihedral_angle_4_deg | 15.034 |
r_dihedral_angle_1_deg | 5.023 |
r_scangle_it | 1.411 |
r_angle_refined_deg | 1.104 |
r_scbond_it | 0.828 |
r_mcangle_it | 0.598 |
r_mcbond_it | 0.347 |
r_symmetry_hbond_refined | 0.333 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8228 |
Nucleic Acid Atoms | |
Solvent Atoms | 47 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |