7FZJ

Crystal Structure of human FABP4 in complex with 3-cyclohexyl-2-ethylsulfanyl-6-hydroxypyrimidin-4-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherinhouse model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368
Crystal Properties
Matthews coefficientSolvent content
2.2144.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.078α = 90
b = 53.736β = 90
c = 74.809γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.700030SLSX10SA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2543.6499.80.0380.0380.04115.756.533769023.464
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)RedundancyNumber Unique Reflections (All)
11.251.2899.61.7241.870.5461.16.682

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTinhouse model1.2543.6434215183695.660.16080.15840.2065RANDOM23.536
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]
-0.33-0.310.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.212
r_sphericity_free28.315
r_sphericity_bonded18.107
r_dihedral_angle_4_deg17.454
r_dihedral_angle_3_deg14.915
r_rigid_bond_restr7.501
r_dihedral_angle_1_deg5.963
r_angle_refined_deg2.569
r_angle_other_deg1.034
r_chiral_restr0.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.212
r_sphericity_free28.315
r_sphericity_bonded18.107
r_dihedral_angle_4_deg17.454
r_dihedral_angle_3_deg14.915
r_rigid_bond_restr7.501
r_dihedral_angle_1_deg5.963
r_angle_refined_deg2.569
r_angle_other_deg1.034
r_chiral_restr0.161
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1046
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms117

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing