4GTS
Engineered RabGGTase in complex with BMS analogue 16
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3DSS |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 285 | RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.31 | 46.83 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 66.636 | α = 90 |
b = 91.366 | β = 90 |
c = 114.093 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU | 2009-04-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.45 | 20 | 98.3 | 0.072 | 17.4 | 3.9 | 26269 | 25813 | 36.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.45 | 2.55 | 97.8 | 0.378 | 4.1 | 3.9 |
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 | 3DSS | 2.45 | 19.99 | 26269 | 24553 | 1259 | 98.51 | 0.18582 | 0.18264 | 0.24771 | RANDOM | 36.071 |
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] | |
0.39 | -0.05 | -0.34 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.872 |
r_dihedral_angle_4_deg | 18.024 |
r_dihedral_angle_3_deg | 16.89 |
r_dihedral_angle_1_deg | 6.05 |
r_angle_other_deg | 4.214 |
r_scangle_it | 3.933 |
r_scbond_it | 2.778 |
r_mcangle_it | 1.742 |
r_angle_refined_deg | 1.544 |
r_mcbond_it | 1.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4994 |
Nucleic Acid Atoms | |
Solvent Atoms | 181 |
Heterogen Atoms | 46 |
Software
Software | |
---|---|
Software Name | Purpose |
MOSFLM | data reduction |
PHASES | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |