7EUV

X-ray structure of high-strength hydrogel-grown FABP3 crystal soaked in 50% DMSO solution containing Flurbiprofen


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.1M Tris-HCl (pH8.5), 50% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.1743.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.23α = 90
b = 69.572β = 90
c = 34.017γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2014-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.800SPring-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
11.285098.40.05111.85.933454
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)
11.281.30.462.1

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 REPLACEMENTTHROUGHOUT3WVM1.2817.6331736169498.530.145750.143580.18912RANDOM16.223
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]
-0.06-0.10.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.245
r_dihedral_angle_4_deg16.433
r_dihedral_angle_3_deg14.579
r_dihedral_angle_1_deg7.132
r_long_range_B_refined4.206
r_long_range_B_other3.948
r_rigid_bond_restr3.838
r_scangle_other3.596
r_scbond_it3.183
r_scbond_other3.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.245
r_dihedral_angle_4_deg16.433
r_dihedral_angle_3_deg14.579
r_dihedral_angle_1_deg7.132
r_long_range_B_refined4.206
r_long_range_B_other3.948
r_rigid_bond_restr3.838
r_scangle_other3.596
r_scbond_it3.183
r_scbond_other3.183
r_mcangle_other2.615
r_mcangle_it2.614
r_mcbond_it2.167
r_mcbond_other2.142
r_angle_refined_deg2.113
r_angle_other_deg1.553
r_chiral_restr0.102
r_bond_refined_d0.017
r_gen_planes_refined0.012
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 Atoms1041
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms36

Software

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