4NC6
Tbc domain of human rab gtpase-activating protein 1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 292 | 27%(W/V) PEG2000 MME, 100MM NA ACETATE , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.98 | 37.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.15 | α = 90 |
b = 51.39 | β = 90 |
c = 132.22 | 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 315r | 2010-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.9797 | ESRF | BM30A |
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 | 99.2 | 0.067 | 23.1 | 3.4 | 27834 | 27834 | 58.8 |
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 | 1.85 | 91.5 | 0.685 | 2.45 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3HZJ | 1.8 | 29.56 | 26432 | 26432 | 1402 | 99.16 | 0.16244 | 0.16244 | 0.15958 | 0.21492 | RANDOM | 17.18 |
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] | |
-0.28 | -0.39 | 0.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.495 |
r_dihedral_angle_4_deg | 25.561 |
r_dihedral_angle_3_deg | 14.706 |
r_dihedral_angle_1_deg | 5.407 |
r_angle_refined_deg | 1.811 |
r_angle_other_deg | 0.955 |
r_chiral_restr | 0.119 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2407 |
Nucleic Acid Atoms | |
Solvent Atoms | 294 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |