6R3V
Crystal Structure of RhoA-GDP-Pi in Complex with RhoGAP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | Equal amounts of reservoir solution containing 18% PEG2000 MME, 100 mM MES, pH 6.0, 10 mM MgCl2, 3 mM DTT, 3 mM NaN3, 120 mM ammonium sulphate and stock solution of the RhoA/RhoGAP protein complex at 800 mM in 20 mM Tris.HCl, pH 7.4, with 2 mM AlCl3, 10 mM MgCl2, and 20 mM NaF. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 114.06 | α = 90 |
b = 122.78 | β = 90 |
c = 67.19 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | PIXEL | DECTRIS PILATUS 6M-F | 2015-05-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91732 | Diamond | I04-1 |
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 | 1.75 | 43.48 | 100 | 0.04 | 19.1 | 6.7 | 47885 | 1.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.75 | 1.78 | 99.9 | 1.3 | 1.56 | 0.679 | 1.4 | 6.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | WWPDB ENTRY 1OXT | 1.75 | 43.48 | 45459 | 2407 | 99.94 | 0.17849 | 0.17694 | 0.20681 | RANDOM | 38.633 |
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] | |
1.99 | 0.43 | -2.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.81 |
r_dihedral_angle_4_deg | 22.435 |
r_dihedral_angle_3_deg | 12.072 |
r_dihedral_angle_1_deg | 5.505 |
r_mcangle_it | 3.848 |
r_scbond_it | 3.598 |
r_mcbond_it | 2.836 |
r_mcbond_other | 2.836 |
r_angle_refined_deg | 1.761 |
r_angle_other_deg | 1.022 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2927 |
Nucleic Acid Atoms | |
Solvent Atoms | 254 |
Heterogen Atoms | 59 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |