7X48

The 0.86 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with pelargonic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Tris-HCl (pH8.0), 45% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1743.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.584α = 90
b = 69.875β = 90
c = 33.858γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.800SPring-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
10.8643.0299.40.0798.411.5109782
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)
10.860.870.4021.8

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 REPLACEMENTTHROUGHOUT3WVM0.8628.79104225548499.360.113230.112460.12744RANDOM9.816
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]
0.23-0.18-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.518
r_dihedral_angle_4_deg13.552
r_dihedral_angle_3_deg12.193
r_dihedral_angle_1_deg6.658
r_long_range_B_refined3.977
r_rigid_bond_restr3.89
r_long_range_B_other3.771
r_scangle_other3.458
r_scbond_it3.092
r_scbond_other3.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.518
r_dihedral_angle_4_deg13.552
r_dihedral_angle_3_deg12.193
r_dihedral_angle_1_deg6.658
r_long_range_B_refined3.977
r_rigid_bond_restr3.89
r_long_range_B_other3.771
r_scangle_other3.458
r_scbond_it3.092
r_scbond_other3.091
r_mcangle_it2.566
r_mcangle_other2.565
r_mcbond_it2.367
r_mcbond_other2.367
r_angle_refined_deg1.844
r_angle_other_deg1.554
r_chiral_restr0.079
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms1040
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms30

Software

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