5SGI
Crystal Structure of human phosphodiesterase 10 in complex with 6-(3-methylphenoxy)-2-(4-pyridin-2-ylpiperazin-1-yl)-9H-purine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.65 | 53.6 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 135.86 | α = 90 |
b = 135.86 | β = 90 |
c = 235.3 | 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2008-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.999800 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.97 | 41.6 | 99 | 0.056 | 0.07 | 0.998 | 13.65 | 2.844 | 112916 | 39.246 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.97 | 2.02 | 93.9 | 0.867 | 1.087 | 0.489 | 1.19 | 2.53 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | inhouse model | 1.97 | 41.63 | 92741 | 4869 | 85.5 | 0.1842 | 0.1816 | 0.2347 | RANDOM | 33.716 |
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] | |
-0.08 | -0.04 | -0.08 | 0.26 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.287 |
r_dihedral_angle_4_deg | 21.028 |
r_dihedral_angle_3_deg | 17.838 |
r_dihedral_angle_1_deg | 15.213 |
r_mcangle_it | 4.202 |
r_mcbond_it | 3.129 |
r_mcbond_other | 3.127 |
r_angle_refined_deg | 1.852 |
r_angle_other_deg | 1.44 |
r_chiral_restr | 0.098 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 10175 |
Nucleic Acid Atoms | |
Solvent Atoms | 686 |
Heterogen Atoms | 136 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |