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Human PPARgamma ligand-binding domain R288A mutant in complex with imatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 296 2.2 M sodium malonate (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.928 α = 90 b = 52.779 β = 90 c = 53.438 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS 2M-F 2018-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 50 99.9 0.059 30.1 6.8 10176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 99.6 0.679
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 FREE R-VALUE 6JQ7 2.752 30.002 9680 459 95.482 0.222 0.2205 0.2245 0.2563 0.2538 44.711
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] 0.559 -0.126 -0.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.657 r_dihedral_angle_4_deg 19.772 r_dihedral_angle_3_deg 16.702 r_lrange_it 9.128 r_lrange_other 9.126 r_dihedral_angle_1_deg 5.935 r_scangle_it 5.87 r_scangle_other 5.869 r_mcangle_it 5.367 r_mcangle_other 5.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.657 r_dihedral_angle_4_deg 19.772 r_dihedral_angle_3_deg 16.702 r_lrange_it 9.128 r_lrange_other 9.126 r_dihedral_angle_1_deg 5.935 r_scangle_it 5.87 r_scangle_other 5.869 r_mcangle_it 5.367 r_mcangle_other 5.366 r_scbond_it 3.553 r_scbond_other 3.552 r_mcbond_it 3.209 r_mcbond_other 3.208 r_chiral_restr_other 1.719 r_angle_refined_deg 1.389 r_angle_other_deg 1.344 r_symmetry_xyhbond_nbd_refined 0.339 r_symmetry_nbd_refined 0.21 r_nbd_refined 0.209 r_nbd_other 0.203 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.096 r_chiral_restr 0.054 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2216 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing