1XQ6
X-ray Structure of Gene Product from Arabidopsis Thaliana At5g02240
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 10 MG/ML PROTEIN, 28 PERCENT PEG 4K, 0.034 M SODIUM MALONATE, 0.10 M BISTRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
2 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 10 MG/ML PROTEIN, 24 PERCENT PEG 4K, 0.136 M SODIUM MALONATE, 0.10 M BISTRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 46.75 | α = 90 |
b = 69.799 | β = 96.01 |
c = 83.828 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 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 | CCD | MAR CCD 165 mm | bent cylindrical Si-mirror (Rh coating) | 2004-08-09 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | bent cylindrical Si-mirror (Rh coating) | 2004-08-08 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 0.9793 | APS | 14-ID-B |
2 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 0.9794, 0.9790, 0.9637 | APS | 14-ID-B |
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 | 1.8 | 23.565 | 93.9 | 0.043 | 19.7 | 5.2 | 52253 |
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) | |||||||||||
1.8 | 1.86 | 87.3 | 0.693 | 2.67 | 5 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.8 | 23.57 | 47341 | 2445 | 95.167 | 0.221 | 0.221 | 0.2183 | 0.2776 | RANDOM | 32.229 |
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] | |
-1.807 | 0.272 | -0.278 | 2.141 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.077 |
r_dihedral_angle_3_deg | 16.825 |
r_dihedral_angle_4_deg | 15.454 |
r_dihedral_angle_1_deg | 7.072 |
r_scangle_it | 6.381 |
r_scbond_it | 4.81 |
r_mcangle_it | 2.864 |
r_angle_refined_deg | 1.833 |
r_mcbond_it | 1.808 |
r_nbtor_refined | 0.31 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3814 |
Nucleic Acid Atoms | |
Solvent Atoms | 400 |
Heterogen Atoms | 96 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
ARP/wARP | model building |