3HZJ
Crystal structure of the RabGAP domain of the RABGAP1L protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6 | 291 | 16% PEG3350, 0.2M potassium chloride, 1:100 (w/w) Dispase., pH 6.0, vapor diffusion, hanging drop, temperature 291K | |
2 | 5.8 | 291 | 15% PEG3350, 0.2M potassium chloride, 1:100 (w/w) Dispase., pH 5.8, vapor diffusion, hanging drop, temperature 291K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 48.086 | α = 90 |
b = 64.571 | β = 90 |
c = 290.255 | γ = 90 |
Symmetry | |
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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 | CCD | MARCCD 300 | 2009-05-18 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | MARCCD 300 | 2009-05-17 | 2009-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.92015 | CLSI | 08ID-1 |
2 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97959 | CLSI | 08ID-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | ||||||||
1,2 | 2.3 | 30 | 88.4 | 0.053 | 31.893 | 3.5 | 38070 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.3 | 2.38 | 49.8 | 0.233 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution 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 | SAD | 2.3 | 20 | 38070 | 1191 | 92.3 | 0.245 | 0.244 | 0.274 | THIN SHELLS (SFTOOLS) | 43.62 |
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] | |
0.337 | 1.886 | -2.224 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.129 |
r_dihedral_angle_4_deg | 16.103 |
r_dihedral_angle_3_deg | 14.336 |
r_dihedral_angle_1_deg | 4.937 |
r_scangle_it | 2.255 |
r_scbond_it | 1.754 |
r_angle_refined_deg | 1.117 |
r_angle_other_deg | 0.875 |
r_mcangle_it | 0.706 |
r_mcbond_it | 0.361 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6428 |
Nucleic Acid Atoms | |
Solvent Atoms | 13 |
Heterogen Atoms | 32 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |