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Structure of the complex between the F360L PPARgamma mutant and the ligand LT175 (space group I222)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293 0.35M Na-phosphate, 0.65 M K-phosphate., pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.5 64.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.17 α = 90 b = 112 β = 90 c = 116.8 γ = 90
Symmetry Space Group I 2 2 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 PSI PILATUS 6M 2013-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.38 50 100 0.11 11.3 6.1 17959 17959
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 2.38 2.49 99.3 0.601 2.9 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3B3K 2.38 80.84 17678 17015 944 99.87 0.18566 0.18348 0.195 0.22585 0.2355 RANDOM 45.65
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] 1.25 -0.18 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_4_deg 16.257 r_dihedral_angle_3_deg 14.74 r_mcangle_it 6.294 r_dihedral_angle_1_deg 5.949 r_scbond_it 4.689 r_mcbond_other 3.925 r_mcbond_it 3.923 r_angle_refined_deg 1.435 r_angle_other_deg 0.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_4_deg 16.257 r_dihedral_angle_3_deg 14.74 r_mcangle_it 6.294 r_dihedral_angle_1_deg 5.949 r_scbond_it 4.689 r_mcbond_other 3.925 r_mcbond_it 3.923 r_angle_refined_deg 1.435 r_angle_other_deg 0.786 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2084 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement AMoRE phasing CNS refinement MOSFLM data reduction SCALA data scaling HKL-2000 data collection