7G20
Crystal Structure of human FABP4 in complex with 1-[(4-methoxyphenyl)methyl]-5-propan-2-yl-5-prop-2-enyl-1,3-diazinane-2,4,6-trione, i.e. SMILES [C@]1(C(=O)N(Cc2ccc(cc2)OC)C(=O)NC1=O)(CC=C)C(C)C with IC50=1.1 microM
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.21 | 44.23 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 32.628 | α = 90 |
b = 53.936 | β = 90 |
c = 75.312 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | PSI PILATUS 6M | 2011-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.000020 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.12 | 37.66 | 98.7 | 0.055 | 0.055 | 0.052 | 0.998 | 17.16 | 5.64 | 51037 | 14.957 |
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 | 1.12 | 1.15 | 87.9 | 0.35 | 0.396 | 0.92 | 4.75 | 4.461 |
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 | 1.12 | 37.66 | 47606 | 2530 | 97.09 | 0.1443 | 0.143 | 0.1675 | RANDOM | 14.755 |
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] | |
0.41 | -0.25 | -0.16 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.173 |
r_sphericity_free | 18.082 |
r_dihedral_angle_4_deg | 16.18 |
r_dihedral_angle_3_deg | 12.017 |
r_sphericity_bonded | 9.983 |
r_dihedral_angle_1_deg | 6.365 |
r_rigid_bond_restr | 5.995 |
r_angle_refined_deg | 2.315 |
r_angle_other_deg | 0.907 |
r_chiral_restr | 0.144 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1040 |
Nucleic Acid Atoms | |
Solvent Atoms | 173 |
Heterogen Atoms | 63 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |