6L96

Structure of PPARalpha-LBD/pemafibrate/SRC1 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HYK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2951.2 M ammonium sulfate and 0.1M bis-tris-HCl (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.9758.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.736α = 90
b = 82.736β = 90
c = 177.521γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2019-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
13.245.71000.080.99620.85.922457
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.261000.6780.81.56.1

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 REPLACEMENTTHROUGHOUT5HYK3.245.671162754499.940.190250.187270.25272RANDOM101.892
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.668
r_dihedral_angle_3_deg21.189
r_dihedral_angle_4_deg17.717
r_long_range_B_refined16.244
r_long_range_B_other16.243
r_scangle_other13.364
r_mcangle_it12.732
r_mcangle_other12.73
r_scbond_it8.836
r_scbond_other8.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.668
r_dihedral_angle_3_deg21.189
r_dihedral_angle_4_deg17.717
r_long_range_B_refined16.244
r_long_range_B_other16.243
r_scangle_other13.364
r_mcangle_it12.732
r_mcangle_other12.73
r_scbond_it8.836
r_scbond_other8.835
r_mcbond_it8.613
r_mcbond_other8.609
r_dihedral_angle_1_deg6.555
r_angle_refined_deg1.642
r_angle_other_deg1.193
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4124
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms72

Software

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