7G13

Crystal Structure of human FABP4 binding site mutated to that of FABP5 in complex with 4-[[3-(3-cyclopropyl-1,2,4-oxadiazol-5-yl)-4,5,6,7-tetrahydro-1-benzothiophen-2-yl]carbamoyl]-3,6-dihydro-2H-pyran-5-carboxylic acid


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
2.0539.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.141α = 90
b = 53.024β = 90
c = 72.169γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000000SLSX10SA

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
11.1542.7398.90.0930.0930.1170.99810.496.034420015.027
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)
11.151.18961.3761.5060.4941.386.018

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 model1.1542.7339948215694.340.15990.15790.1981RANDOM13.857
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]
0.40.67-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.908
r_sphericity_free24.599
r_dihedral_angle_4_deg16.304
r_dihedral_angle_3_deg13.911
r_sphericity_bonded12.86
r_dihedral_angle_1_deg6.417
r_rigid_bond_restr5.127
r_angle_other_deg3.346
r_angle_refined_deg2.283
r_chiral_restr0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.908
r_sphericity_free24.599
r_dihedral_angle_4_deg16.304
r_dihedral_angle_3_deg13.911
r_sphericity_bonded12.86
r_dihedral_angle_1_deg6.417
r_rigid_bond_restr5.127
r_angle_other_deg3.346
r_angle_refined_deg2.283
r_chiral_restr0.134
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1012
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms62

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing