7WPU

The 0.95 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with undecanoic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1M Glycin-NaOH (pH9.0), 55% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1643.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.657α = 90
b = 69.908β = 90
c = 33.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.9000SPring-8BL38B1

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
10.9543.0599.10.06712.581542
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)
10.950.970.3722.6

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 REPLACEMENTTHROUGHOUT3WVM0.9524.2877391408999.020.104050.103560.11316RANDOM10.831
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]
0.1-0.06-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.528
r_dihedral_angle_4_deg14.891
r_dihedral_angle_3_deg14.297
r_rigid_bond_restr6.212
r_dihedral_angle_1_deg6.176
r_long_range_B_refined5.459
r_scangle_other4.864
r_long_range_B_other4.712
r_scbond_other4.398
r_scbond_it4.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.528
r_dihedral_angle_4_deg14.891
r_dihedral_angle_3_deg14.297
r_rigid_bond_restr6.212
r_dihedral_angle_1_deg6.176
r_long_range_B_refined5.459
r_scangle_other4.864
r_long_range_B_other4.712
r_scbond_other4.398
r_scbond_it4.34
r_angle_other_deg2.094
r_angle_refined_deg2.013
r_mcangle_other1.686
r_mcangle_it1.685
r_mcbond_it1.286
r_mcbond_other1.273
r_chiral_restr0.097
r_bond_refined_d0.021
r_bond_other_d0.021
r_gen_planes_refined0.014
r_gen_planes_other0.003
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 Atoms1041
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms42

Software

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