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PPARgamma Ligand binding domain in complex with piperine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VV3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1 M Tris-HCl, 0.7 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.43 α = 90 b = 62.02 β = 102.09 c = 119.49 γ = 90
Symmetry Space Group C 1 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 6M 2024-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.36 45.68 99.6 0.058 0.04 0.995 9.2 3.1 27580
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.45 0.344 0.236 0.936 2.6 2.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2VV3 2.36 45.68 27570 1374 99.391 0.203 0.2006 0.1997 0.2547 0.2601 68.131
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] 2.682 0.29 -0.376 -2.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.094 r_dihedral_angle_6_deg 15.525 r_dihedral_angle_2_deg 11.649 r_lrange_it 10.089 r_lrange_other 10.089 r_scangle_it 8.318 r_scangle_other 8.317 r_dihedral_angle_1_deg 6.064 r_mcangle_it 5.985 r_mcangle_other 5.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.094 r_dihedral_angle_6_deg 15.525 r_dihedral_angle_2_deg 11.649 r_lrange_it 10.089 r_lrange_other 10.089 r_scangle_it 8.318 r_scangle_other 8.317 r_dihedral_angle_1_deg 6.064 r_mcangle_it 5.985 r_mcangle_other 5.985 r_scbond_it 5.658 r_scbond_other 5.657 r_mcbond_it 4.336 r_mcbond_other 4.335 r_angle_refined_deg 2.2 r_angle_other_deg 0.721 r_nbd_refined 0.254 r_nbd_other 0.252 r_chiral_restr_other 0.238 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.174 r_ncsr_local_group_1 0.16 r_symmetry_nbd_refined 0.146 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4054 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction REFMAC phasing