7VB1

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.1M Mes-NaOH (pH6.5), 55% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1342.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.511α = 90
b = 69.365β = 90
c = 33.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2014-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.800SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
10.95099.50.0328.68.894324
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.90.9299.70.232.26.9

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 REPLACEMENTTHROUGHOUT3WVM0.926.3889628463799.510.115250.114640.12731RANDOM10.928
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]
-0.350.170.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.588
r_dihedral_angle_4_deg15.173
r_dihedral_angle_3_deg13.293
r_rigid_bond_restr9.384
r_dihedral_angle_1_deg6.16
r_scbond_it3.89
r_scbond_other3.89
r_long_range_B_refined3.802
r_scangle_other3.774
r_long_range_B_other3.442
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.588
r_dihedral_angle_4_deg15.173
r_dihedral_angle_3_deg13.293
r_rigid_bond_restr9.384
r_dihedral_angle_1_deg6.16
r_scbond_it3.89
r_scbond_other3.89
r_long_range_B_refined3.802
r_scangle_other3.774
r_long_range_B_other3.442
r_angle_refined_deg1.997
r_mcangle_it1.623
r_mcangle_other1.623
r_angle_other_deg1.549
r_mcbond_it1.269
r_mcbond_other1.245
r_chiral_restr0.104
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms1041
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms55

Software

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