7G1D
Crystal Structure of human FABP4 in complex with 5-ethyl-6-(3-methoxyphenyl)-3-methyl-2-sulfanylidene-1H-pyrimidin-4-one
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.19 | 43.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.555 | α = 90 |
b = 53.76 | β = 90 |
c = 75.08 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.000020 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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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 | 37.54 | 97.7 | 0.074 | 0.074 | 0.076 | 0.997 | 11.58 | 6.08 | 50371 | 16.528 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 83.4 | 0.715 | 0.803 | 0.786 | 2.78 | 4.798 |
Refinement
Statistics | |||||||||||||||||||
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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 | 37.53 | 46630 | 2461 | 95.35 | 0.1532 | 0.1513 | 0.1874 | RANDOM | 17.751 |
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] | |
0.56 | -0.53 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.562 |
r_sphericity_free | 24.912 |
r_dihedral_angle_4_deg | 17.575 |
r_dihedral_angle_3_deg | 13.444 |
r_sphericity_bonded | 12.8 |
r_dihedral_angle_1_deg | 6.352 |
r_rigid_bond_restr | 6.157 |
r_angle_refined_deg | 2.309 |
r_angle_other_deg | 0.887 |
r_chiral_restr | 0.13 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1046 |
Nucleic Acid Atoms | |
Solvent Atoms | 172 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |