8PA6
Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl 2-aminoethenoadenosine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6YQM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 281 | 12% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.11 | 41.58 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 78.845 | α = 90 |
b = 46.324 | β = 94.799 |
c = 63.971 | 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 | PIXEL | RIGAKU HyPix-6000HE | 2022-09-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | RIGAKU PhotonJet-S | 1.54184 |
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 | 1.58 | 19.101 | 99.9 | 0.074 | 0.082 | 0.035 | 0.998 | 15.3 | 5.4 | 31671 | 8.2 |
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 | 1.58 | 1.61 | 100 | 0.661 | 0.775 | 0.396 | 0.742 | 2.1 | 3.6 |
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 | THROUGHOUT | 1.58 | 19.101 | 31671 | 1625 | 99.912 | 0.15 | 0.1474 | 0.1913 | 10.824 |
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] | |
1.397 | -0.114 | -0.473 | -0.893 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 15.953 |
r_dihedral_angle_3_deg | 14.214 |
r_dihedral_angle_2_deg | 7.088 |
r_dihedral_angle_1_deg | 6.217 |
r_lrange_it | 5.488 |
r_lrange_other | 4.783 |
r_scangle_it | 2.558 |
r_scangle_other | 2.558 |
r_mcangle_it | 1.705 |
r_mcangle_other | 1.704 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1766 |
Nucleic Acid Atoms | |
Solvent Atoms | 390 |
Heterogen Atoms | 36 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
Aimless | data scaling |
MOLREP | phasing |