1R8S
ARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MUTATION OF THE CATALYTIC GLUTAMATE TO LYSINE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1R8R | PDB ENTRY 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 289 | 1.88M Ammonium Sulfate, 100mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 51.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.018 | α = 90 |
b = 104.018 | β = 90 |
c = 69.277 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | 0.931 | ESRF | ID14-3 |
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 | 1.46 | 30 | 0.059 | 26.6 | 16 | 75051 | 18.35 |
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 | 1.46 | 1.47 | 97 | 0.462 | 5.9 | 12.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48) | 1.46 | 28.87 | 75051 | 71299 | 3744 | 99.91 | 0.15941 | 0.15885 | 0.1698 | RANDOM | 12.525 |
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] | |
-0.05 | -0.02 | -0.05 | 0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.153 |
r_scangle_it | 4.08 |
r_scbond_it | 2.529 |
r_mcangle_it | 1.68 |
r_angle_refined_deg | 1.421 |
r_mcbond_it | 0.881 |
r_angle_other_deg | 0.87 |
r_symmetry_vdw_refined | 0.56 |
r_symmetry_vdw_other | 0.31 |
r_nbd_other | 0.246 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2806 |
Nucleic Acid Atoms | |
Solvent Atoms | 350 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
XDS | data scaling |
CCP4 | phasing |