3IKG
Structure-Based Design of Novel PIN1 Inhibitors (I)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 286 | 0.2M ammonium sulfate, 0.9M Na Citrate, 5mM TCEP, 100mM HEPES: Compound @ 500uM soaked into apo crystal for 60hrs. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 286K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.77 | 38.35 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 118.255 | α = 90 |
b = 36.53 | β = 100.4 |
c = 51.32 | 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 | 110 | IMAGE PLATE | MAR scanner 345 mm plate | OSMIC BLUE | 2000-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R | 1.0 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.86 | 10 | 99.1 | 0.061 | 20.7 | 4.39 | 18140 | 18140 | 1 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.86 | 1.93 | 91.5 | 0.404 | 0.404 | 3.6 | 4.2 | 1684 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | DIFFERENCE FOURIER | PDB ENTRY 3IK8 Apo PPIase K7782Q | 1.86 | 10 | 18140 | 18140 | 99.6 | 0.2062 | 0.2062 | 0.2062 | None selected |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
2001 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_similar_adp_cmpnt | 0.076 |
s_non_zero_chiral_vol | 0.035 |
s_zero_chiral_vol | 0.029 |
s_from_restr_planes | 0.0255 |
s_angle_d | 0.02 |
s_anti_bump_dis_restr | 0.019 |
s_bond_d | 0.005 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1781 |
Nucleic Acid Atoms | |
Solvent Atoms | 167 |
Heterogen Atoms | 54 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data collection |
SHELX | model building |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |