1ZBD
STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8 | pH 8.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.64 | 52.62 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 89.315 | α = 90 |
b = 95.619 | β = 94.49 |
c = 47.715 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
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 | MIRRORS | 1998-05-31 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.9789, 0.9793, 0.9879 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.6 | 90 | 98.5 | 0.053 | 0.049 | 17.9 | 2 | 23889 | 35.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.6 | 2.7 | 97.8 | 0.3 | 0.22 | 0.3 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.6 | 90 | 23478 | 2213 | 96.8 | 0.226 | 0.226 | 0.263 | RANDOM | 51.5 |
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] | |
6.16 | -1.62 | 1.18 | -7.32 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.5 |
c_scangle_it | 12.39 |
c_scbond_it | 9.85 |
c_mcangle_it | 8.8 |
c_mcbond_it | 6.52 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.89 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2445 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 35 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |