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Crystal structure of the complex of F360L PPARgamma mutant with the ligand LT175
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 7 293 3.3 M Sodium Formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.4 63.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.41 α = 90 b = 112.46 β = 90 c = 117.74 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 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 0.973 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 2.28 50 99.9 0.088 18.9 39713 39713
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 2.28 2.5 99.9 0.424 4.8
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 2.28 117.74 39204 37723 1956 99.74 0.21309 0.21091 0.2213 0.2576 0.2594 RANDOM 43.074
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] 2.54 -0.54 -2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.558 r_dihedral_angle_3_deg 17.65 r_mcangle_it 16.914 r_dihedral_angle_4_deg 16.814 r_scbond_it 12.487 r_mcbond_other 10.935 r_mcbond_it 10.933 r_dihedral_angle_1_deg 6.348 r_angle_refined_deg 1.506 r_angle_other_deg 1.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.558 r_dihedral_angle_3_deg 17.65 r_mcangle_it 16.914 r_dihedral_angle_4_deg 16.814 r_scbond_it 12.487 r_mcbond_other 10.935 r_mcbond_it 10.933 r_dihedral_angle_1_deg 6.348 r_angle_refined_deg 1.506 r_angle_other_deg 1.096 r_chiral_restr 0.114 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 4015 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement AMoRE phasing CNS refinement MOSFLM data reduction SCALA data scaling HKL-2000 data collection