7WDJ

The 0.90 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with linoleic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WVM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M Hepes-NaOH (pH7.5), 60% PEG 400 or 0.1M Glycine-NaOH (pH9.0), 60% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1542.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.62α = 90
b = 69.733β = 90
c = 33.617γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.75000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
10.94399.50.0659.111.995206
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.90.920.3873.2

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 REPLACEMENTTHROUGHOUT3WVM0.930.390365477399.40.119020.118630.12647RANDOM11.289
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]
0.1-0.05-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.463
r_dihedral_angle_4_deg13.962
r_dihedral_angle_3_deg12.02
r_rigid_bond_restr11.733
r_scangle_other8.188
r_long_range_B_refined7.179
r_scbond_it7.034
r_scbond_other7.016
r_long_range_B_other6.996
r_dihedral_angle_1_deg6.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.463
r_dihedral_angle_4_deg13.962
r_dihedral_angle_3_deg12.02
r_rigid_bond_restr11.733
r_scangle_other8.188
r_long_range_B_refined7.179
r_scbond_it7.034
r_scbond_other7.016
r_long_range_B_other6.996
r_dihedral_angle_1_deg6.004
r_mcbond_it5.783
r_mcbond_other5.756
r_mcangle_other5.104
r_mcangle_it5.086
r_angle_refined_deg2.298
r_angle_other_deg1.656
r_chiral_restr0.11
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_bond_other_d0.004
r_gen_planes_other0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1039
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing