7GSB
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000438a
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.34 | 63.15 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 89.937 | α = 90 |
b = 89.937 | β = 90 |
c = 106.782 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 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 | DECTRIS PILATUS 6M | 2016-09-25 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92819 | Diamond | I04-1 |
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 | 1.72 | 62.927 | 99.9 | 0.055 | 0.062 | 0.999 | 16.45 | 102049 | -3 | 36.892 |
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 | 1.72 | 1.83 | 99.4 | 1.027 | 1.143 | 0.519 | 1.41 |
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 | 1.72 | 44.97 | 51111 | 2099 | 99.9 | 0.1899 | 0.1885 | 0.2249 | RANDOM | 37.725 |
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] | |
0.54 | 0.27 | 0.54 | -1.74 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.673 |
r_dihedral_angle_4_deg | 20.313 |
r_dihedral_angle_3_deg | 14.735 |
r_dihedral_angle_1_deg | 6.461 |
r_mcangle_it | 4.572 |
r_mcbond_other | 3.623 |
r_mcbond_it | 3.617 |
r_angle_refined_deg | 1.69 |
r_angle_other_deg | 1.345 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2317 |
Nucleic Acid Atoms | |
Solvent Atoms | 244 |
Heterogen Atoms | 61 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
XDS | data reduction |