8S2X
SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROFLUIDIC | 7 | 294 | 600 mM Sodium citrate and 100 mM HEPES pH 7 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.99 | 58.86 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 180.3 | α = 90 |
b = 180.3 | β = 90 |
c = 119.2 | γ = 120 |
Symmetry | |
---|---|
Space Group | H 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | PIXEL | PSI JUNGFRAU 4M | 2023-01-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.07 | ESRF | ID29 |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | SOS Chip | fixed target |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 20635 | 20827 | 245400 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.5 | 94.75 | 100 | 0.96 | 5 | 44.2 | 50011 | 45.27 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.5 | 2.54 | 100 | 0.27 | 0.8 | 44.2 |
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-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.5 | 65.396 | 50003 | 2510 | 99.984 | 0.16 | 0.1584 | 0.1883 | 59.187 |
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] | |
0.006 | 0.003 | 0.006 | -0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 14.633 |
r_dihedral_angle_6_deg | 14.104 |
r_lrange_it | 11.962 |
r_lrange_other | 11.951 |
r_scangle_it | 9.728 |
r_scangle_other | 9.702 |
r_dihedral_angle_2_deg | 9.081 |
r_mcangle_it | 7.523 |
r_mcangle_other | 7.523 |
r_dihedral_angle_1_deg | 6.5 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 8088 |
Nucleic Acid Atoms | |
Solvent Atoms | 186 |
Heterogen Atoms | 72 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
MOLREP | phasing |