3AKN

X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IFB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727730-45% w/v PEG 2000, 0.1M Tris pH 7.0, 0.2M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.59α = 90
b = 50.59β = 90
c = 97.452γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMirrors2008-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.954Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.644.91000.0560.0574227.71748017480220.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.691000.3820.38910.128.12499

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2IFB1.644.92165401654088099.990.226420.224830.25671RANDOM19.348
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]
0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.415
r_dihedral_angle_4_deg17.712
r_dihedral_angle_3_deg12.233
r_dihedral_angle_1_deg6.071
r_scangle_it3.834
r_scbond_it2.456
r_mcangle_it1.615
r_angle_refined_deg1.377
r_mcbond_it0.96
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.415
r_dihedral_angle_4_deg17.712
r_dihedral_angle_3_deg12.233
r_dihedral_angle_1_deg6.071
r_scangle_it3.834
r_scbond_it2.456
r_mcangle_it1.615
r_angle_refined_deg1.377
r_mcbond_it0.96
r_nbtor_refined0.308
r_nbd_refined0.193
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.13
r_xyhbond_nbd_refined0.11
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1047
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms30

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling