2Y8E
Crystal structure of D. melanogaster Rab6 GTPase bound to GMPPNP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YZQ | PDB ENTRY 1YZQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 2.4 M AMMONIUM SULPHATE, 0.1 M IMIDAZOLE PH 8.0, 2.5% PEG 400, 2.5% DMSO AND 3% TRIMETHYLAMINE N-OXIDE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.92 | 35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 116.52 | α = 90 |
b = 42.71 | β = 133.12 |
c = 86.86 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | CCD | ADSC CCD | 2010-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 |
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 | 1.39 | 31.7 | 97.4 | 0.05 | 9.7 | 3.5 | 61395 | 12.326 |
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 | 1.39 | 1.47 | 95.3 | 0.28 | 4.4 | 3.4 |
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 | PDB ENTRY 1YZQ | 1.39 | 63.4 | 58225 | 3121 | 97.32 | 0.14607 | 0.14458 | 0.17296 | RANDOM | 11.573 |
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] | |
0.26 | -0.29 | -0.15 | -0.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.24 |
r_dihedral_angle_4_deg | 17.056 |
r_dihedral_angle_3_deg | 12.006 |
r_dihedral_angle_1_deg | 5.947 |
r_scangle_it | 5.236 |
r_scbond_it | 3.503 |
r_mcangle_it | 2.44 |
r_angle_refined_deg | 1.561 |
r_mcbond_it | 1.478 |
r_rigid_bond_restr | 1.346 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2682 |
Nucleic Acid Atoms | |
Solvent Atoms | 226 |
Heterogen Atoms | 81 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |