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Human PPARgamma ligand binding dmain complexed with S35
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VN2
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 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.823 α = 90 b = 53.286 β = 90 c = 53.74 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 CCD ADSC QUANTUM 315r 2013-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.00002 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 99.5 41.1 5.6 22810
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 2.1 2.14 100 0.591 3.6 5.6
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 3VN2 2.1 30 21608 1113 99.46 0.21237 0.2109 0.2176 0.24247 0.2504 RANDOM 55.293
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] -1.21 0.6 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.378 r_dihedral_angle_4_deg 19.429 r_dihedral_angle_3_deg 13.878 r_long_range_B_refined 9.851 r_long_range_B_other 9.809 r_scangle_other 6.534 r_mcangle_it 5.056 r_mcangle_other 5.055 r_dihedral_angle_1_deg 4.855 r_scbond_it 3.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.378 r_dihedral_angle_4_deg 19.429 r_dihedral_angle_3_deg 13.878 r_long_range_B_refined 9.851 r_long_range_B_other 9.809 r_scangle_other 6.534 r_mcangle_it 5.056 r_mcangle_other 5.055 r_dihedral_angle_1_deg 4.855 r_scbond_it 3.965 r_scbond_other 3.963 r_mcbond_it 3.321 r_mcbond_other 3.321 r_angle_refined_deg 1.482 r_angle_other_deg 1.233 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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 2245 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing