2G77
Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 7 | 277 | 10~15% polyethylene glycol 6000, 100 mM Sodium Acetate, 10% Glycerol, 20 mM NaF, 2mM AlCl3, 50 mM HEPES, pH7.0, EVAPORATION, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.2 | α = 90 |
b = 94.526 | β = 90 |
c = 102.561 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 4 | 2005-02-09 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | CCD | ADSC QUANTUM 315 | 2005-02-09 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.979026 | NSLS | X29A |
2 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9793, 0.9790, 0.9670 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.26 | 50 | 99 | 0.065 | 9.9 | 5 | 62674 | 33046 | 37.6 | 1017 | 27 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.26 | 2.34 | 99.9 | 0.354 | 4.93 | 5.1 | 6309 |
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 | MAD | THROUGHOUT | 2.26 | 8 | 30553 | 1634 | 98.65 | 0.207 | 0.20726 | 0.20524 | 0.24357 | RANDOM | 39.538 |
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] | |
-1.88 | 4.63 | -2.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.869 |
r_dihedral_angle_4_deg | 14.393 |
r_dihedral_angle_3_deg | 14.166 |
r_dihedral_angle_1_deg | 4.713 |
r_scangle_it | 1.32 |
r_angle_refined_deg | 0.987 |
r_mcangle_it | 0.912 |
r_scbond_it | 0.817 |
r_mcbond_it | 0.519 |
r_nbtor_refined | 0.298 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4141 |
Nucleic Acid Atoms | |
Solvent Atoms | 416 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |