2F9M
3D structure of active human Rab11b GTPase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | reservoir solution: 0.1M Tris-HCl pH8.5, 1M lithium sulfate, 0.01M nickel chloride. Protein sample: 68 mg/ml Rab11b-GppNHp, 10mM Tris-HCl pH7.4, 0.1mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.611 | α = 90 |
b = 85.409 | β = 90 |
c = 86.886 | γ = 90 |
Symmetry | |
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Space Group | I 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 | MARRESEARCH | 2004-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE D03B-MX1 | 1.43 | LNLS | D03B-MX1 |
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 | 1.95 | 33.48 | 99.8 | 0.09 | 19.3 | 9.2 | 18222 |
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) | |||||||||||
1.95 | 2.06 | 100 | 0.331 | 6.6 | 9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1.95 | 30 | 18438 | 17437 | 940 | 99.65 | 0.16479 | 0.16479 | 0.16263 | 0.20529 | RANDOM | 17.688 |
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] | |
-0.66 | -0.59 | 1.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.324 |
r_dihedral_angle_3_deg | 14.483 |
r_dihedral_angle_4_deg | 13.887 |
r_dihedral_angle_1_deg | 5.57 |
r_scangle_it | 2.926 |
r_scbond_it | 1.763 |
r_angle_refined_deg | 1.263 |
r_mcangle_it | 1.036 |
r_mcbond_it | 0.56 |
r_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1456 |
Nucleic Acid Atoms | |
Solvent Atoms | 286 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
MOSFLM | data reduction |
CCP4 | data scaling |
AMoRE | phasing |