7FX7

Crystal Structure of human FABP4 with binding site mutated to FABP5 in complex with 5-methylsulfanyl-2-[(4-phenylmethoxy-1H-indazol-3-yl)methylsulfanyl]pyrimidin-4-ol


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
2.0540.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.224α = 90
b = 52.943β = 90
c = 72.326γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-10-22MSINGLE 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
11.1242.7299.20.0860.0860.090.99910.776.084798114.391
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)
11.121.1589.41.1481.2930.4121.394.537

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 model1.1242.7243879233095.670.17140.16920.2132RANDOM11.675
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]
0.61-0.840.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.421
r_sphericity_free19.516
r_dihedral_angle_4_deg15.656
r_dihedral_angle_3_deg12.558
r_sphericity_bonded10.599
r_dihedral_angle_1_deg6.023
r_rigid_bond_restr4.709
r_angle_refined_deg2.02
r_angle_other_deg0.993
r_chiral_restr0.358
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.421
r_sphericity_free19.516
r_dihedral_angle_4_deg15.656
r_dihedral_angle_3_deg12.558
r_sphericity_bonded10.599
r_dihedral_angle_1_deg6.023
r_rigid_bond_restr4.709
r_angle_refined_deg2.02
r_angle_other_deg0.993
r_chiral_restr0.358
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1012
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms36

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing