1Q91
Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor DPB-T
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1MH9 | pdb code 1MH9 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.3 | 298 | PEG 8000, potassium phosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.64 | 53.04 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 73.651 | α = 90 |
b = 73.651 | β = 90 |
c = 106.83 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
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 | ADSC QUANTUM 4 | 2002-01-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9393 | ESRF | ID14-4 |
Data Collection
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | pdb code 1MH9 | 1.6 | 19.77 | 38484 | 38484 | 3859 | 97.7 | 0.186 | 0.186 | 0.206 | RANDOM | 26 |
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] | |
-1.62 | -1.62 | 3.25 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_scbond_it | 26.96 |
c_dihedral_angle_d | 23.9 |
c_scangle_it | 14.32 |
c_mcangle_it | 3.77 |
c_mcbond_it | 3.04 |
c_angle_deg | 2.2 |
c_improper_angle_d | 1.48 |
c_bond_d | 0.026 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1598 |
Nucleic Acid Atoms | |
Solvent Atoms | 328 |
Heterogen Atoms | 34 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |