8PNC
Transcription factor BARHL2 bound to TAAGT DNA sequence
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 8PM5 | chain A |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.8 | 293 | PEG 4000, sodium malonate, sodium acetate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.46 | 52.32 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 39.519 | α = 90 |
b = 123.711 | β = 93.94 |
c = 62.365 | 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 | PIXEL | DECTRIS PILATUS 6M | 2022-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.8856 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.05 | 43.87 | 99.6 | 0.17 | 0.19 | 0.083 | 0.993 | 7.7 | 5.2 | 37375 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.05 | 2.11 | 97.1 | 2.305 | 2.599 | 1.176 | 0.188 | 4.8 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.05 | 39.46 | 35433 | 1912 | 99.6 | 0.2337 | 0.232 | 0.2672 | RANDOM | 41.355 |
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] | |
-1.07 | -0.35 | 1.18 | -0.06 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.717 |
r_dihedral_angle_4_deg | 19.324 |
r_dihedral_angle_3_deg | 15.121 |
r_dihedral_angle_1_deg | 8.041 |
r_angle_refined_deg | 2.397 |
r_angle_other_deg | 1.183 |
r_chiral_restr | 0.204 |
r_gen_planes_refined | 0.013 |
r_bond_refined_d | 0.012 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2085 |
Nucleic Acid Atoms | 1944 |
Solvent Atoms | 351 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |