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Human PPARgamma ligand binding dmain complexed with R35
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 57.5% (v/v) Tacsimate pH7.0
Crystal Properties Matthews coefficient Solvent content 2.91 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.65 α = 90 b = 52.454 β = 90 c = 54.289 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 270 2013-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.00000 PAL/PLS 7A (6B, 6C1)
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 1.85 50 99.7 39.5 4.8 32794
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 1.85 1.88 100 0.437 3 4.8
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 1.85 30 31197 1549 99.6 0.20594 0.20462 0.2142 0.23165 0.2345 RANDOM 39.063
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] -0.81 0.86 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.948 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 12.802 r_long_range_B_refined 7.741 r_long_range_B_other 7.487 r_dihedral_angle_1_deg 5.397 r_scangle_other 4.899 r_mcangle_it 3.982 r_mcangle_other 3.98 r_scbond_it 3.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.948 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 12.802 r_long_range_B_refined 7.741 r_long_range_B_other 7.487 r_dihedral_angle_1_deg 5.397 r_scangle_other 4.899 r_mcangle_it 3.982 r_mcangle_other 3.98 r_scbond_it 3.009 r_scbond_other 3.008 r_mcbond_other 2.612 r_mcbond_it 2.611 r_angle_refined_deg 1.488 r_angle_other_deg 0.981 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 2265 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing