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The ligand-free structure of human PPARgamma LBD R280C mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L8B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 1.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.936 α = 90 b = 61.281 β = 102.424 c = 119.502 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 EIGER X 4M 2017-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 91 1 19.43 5.2 21448
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 89.1 0.88 2.06 5.3
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 6L8B 2.5 27.873 19845 983 85.458 0.218 0.2156 0.2189 0.2645 0.2698 41.205
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] -0.117 -0.141 0.641 -0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.133 r_dihedral_angle_4_deg 17.043 r_dihedral_angle_3_deg 13.791 r_lrange_other 5.873 r_lrange_it 5.871 r_dihedral_angle_1_deg 5.672 r_mcangle_it 3.14 r_mcangle_other 3.139 r_scangle_it 3.059 r_scangle_other 3.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.133 r_dihedral_angle_4_deg 17.043 r_dihedral_angle_3_deg 13.791 r_lrange_other 5.873 r_lrange_it 5.871 r_dihedral_angle_1_deg 5.672 r_mcangle_it 3.14 r_mcangle_other 3.139 r_scangle_it 3.059 r_scangle_other 3.059 r_mcbond_it 1.812 r_mcbond_other 1.812 r_scbond_it 1.735 r_scbond_other 1.734 r_angle_refined_deg 1.216 r_angle_other_deg 1.096 r_symmetry_xyhbond_nbd_refined 0.286 r_symmetry_nbd_refined 0.198 r_nbd_refined 0.191 r_nbd_other 0.183 r_symmetry_nbd_other 0.177 r_xyhbond_nbd_refined 0.16 r_nbtor_refined 0.15 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4136 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing