3JZA
Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from Legionella pneumophila
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.75 | 292 | 0.1 M Sodium citrate, 35% v/v PEG 600, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.756 | α = 90 |
b = 100.756 | β = 90 |
c = 146.36 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 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 225 mm CCD | 2008-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.000000 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.8 | 30 | 98.1 | 0.09 | 21.97 | 40529 | -3 | 33.85 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.9 | 97.1 | 0.456 | 4.7 |
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 | SAD | THROUGHOUT | 1.8 | 29.63 | 40517 | 2005 | 98.13 | 0.202 | 0.201 | 0.234 | RANDOM | 17.349 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-2.79 | -1.4 | -2.79 | 4.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.354 |
r_dihedral_angle_4_deg | 15.583 |
r_dihedral_angle_3_deg | 14.364 |
r_dihedral_angle_1_deg | 6.405 |
r_scangle_it | 4.731 |
r_scbond_it | 3.123 |
r_mcangle_it | 2.067 |
r_angle_refined_deg | 1.829 |
r_mcbond_it | 1.292 |
r_angle_other_deg | 1.05 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2818 |
Nucleic Acid Atoms | |
Solvent Atoms | 246 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
SHARP | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
XDS | data reduction |