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Structure of PPARalpha-LBD/pemafibrate/SRC1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 1.2 M ammonium sulfate and 0.1M bis-tris-HCl (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.97 58.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.736 α = 90 b = 82.736 β = 90 c = 177.521 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 2M 2019-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.2 45.7 100 0.08 0.996 20.8 5.9 22457
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) Redundancy Number Unique Reflections (All) 1 3.2 3.26 100 0.678 0.8 1.5 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HYK 3.2 45.67 11627 544 99.94 0.19025 0.18727 0.1887 0.25272 0.2476 RANDOM 101.892
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 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_3_deg 21.189 r_dihedral_angle_4_deg 17.717 r_long_range_B_refined 16.244 r_long_range_B_other 16.243 r_scangle_other 13.364 r_mcangle_it 12.732 r_mcangle_other 12.73 r_scbond_it 8.836 r_scbond_other 8.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_3_deg 21.189 r_dihedral_angle_4_deg 17.717 r_long_range_B_refined 16.244 r_long_range_B_other 16.243 r_scangle_other 13.364 r_mcangle_it 12.732 r_mcangle_other 12.73 r_scbond_it 8.836 r_scbond_other 8.835 r_mcbond_it 8.613 r_mcbond_other 8.609 r_dihedral_angle_1_deg 6.555 r_angle_refined_deg 1.642 r_angle_other_deg 1.193 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 Atoms Number Protein Atoms 4124 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing