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Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative modulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LMP PDB ENTRY 3LMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 PEG 4000, sodium thiocyanate, Tris-hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.889 α = 90 b = 54.614 β = 92.35 c = 66.797 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS VII 2010-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 1.6 50 99.4 3.5 37110 36869 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 94.8 3 3491
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 PDB ENTRY 3LMP 1.65 20 30353 3392 99.89 0.2035 0.20176 0.2179 0.21878 0.2381 RANDOM 25.561
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] 1.06 -0.3 -0.68 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.587 r_dihedral_angle_4_deg 18.128 r_dihedral_angle_3_deg 11.263 r_dihedral_angle_1_deg 4.37 r_scangle_it 2.741 r_scbond_it 1.613 r_mcangle_it 1.069 r_angle_refined_deg 1.003 r_angle_other_deg 0.804 r_mcbond_it 0.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.587 r_dihedral_angle_4_deg 18.128 r_dihedral_angle_3_deg 11.263 r_dihedral_angle_1_deg 4.37 r_scangle_it 2.741 r_scbond_it 1.613 r_mcangle_it 1.069 r_angle_refined_deg 1.003 r_angle_other_deg 0.804 r_mcbond_it 0.541 r_mcbond_other 0.094 r_chiral_restr 0.056 r_bond_refined_d 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2134 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 39
Software Software Software Name Purpose CrystalClear data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing