7G14
Crystal Structure of human FABP4 in complex with 6-cyclopentyl-N,5-dimethyl-4-phenyl-N-propan-2-yl-3-(1H-tetrazol-5-yl)pyridin-2-amine, i.e. SMILES c1(c(nc(c(c1c1ccccc1)C1=NN=NN1)N(C(C)C)C)C1CCCC1)C with IC50=0.014086 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 |
2.19 | 43.77 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 32.468 | α = 90 |
b = 54.097 | β = 90 |
c = 74.828 | 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 | 2012-05-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.999980 | 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 | 1.2 | 30.77 | 98.9 | 0.034 | 0.034 | 0.037 | 1 | 20.85 | 5.99 | 41217 | 19.708 |
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 | 1.2 | 1.24 | 86.9 | 0.858 | 0.977 | 0.693 | 1.59 | 4.132 |
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 | 1.2 | 30.79 | 37725 | 2019 | 95.52 | 0.1461 | 0.1442 | 0.1835 | RANDOM | 19.251 |
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] | |
-0.03 | 0.35 | -0.32 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.559 |
r_sphericity_free | 27.941 |
r_dihedral_angle_4_deg | 15.096 |
r_dihedral_angle_3_deg | 13.429 |
r_sphericity_bonded | 12.674 |
r_dihedral_angle_1_deg | 6.183 |
r_rigid_bond_restr | 5.129 |
r_angle_refined_deg | 2.009 |
r_angle_other_deg | 0.82 |
r_chiral_restr | 0.125 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1040 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 76 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |