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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-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.03 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.693 α = 90 b = 54.167 β = 91.38 c = 66.218 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 2005-10-25 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) R Sym 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 1.85 50 99.3 0.073 18 3 23474 23317 -3 21.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 100 0.339 2.9 2.9 2306
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LMP 1.9 19.37 21575 2168 99.4 0.228 0.2252 0.254 0.2521 31.8
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] 7.71 -6.36 -3.82 -3.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 2.68 c_mcangle_it 1.87 c_scbond_it 1.77 c_mcbond_it 1.23 c_angle_deg 1.1 c_improper_angle_d 0.75 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.1 c_scangle_it 2.68 c_mcangle_it 1.87 c_scbond_it 1.77 c_mcbond_it 1.23 c_angle_deg 1.1 c_improper_angle_d 0.75 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2190 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 39
Software Software Software Name Purpose CrystalClear data collection CNX refinement HKL-2000 data reduction HKL-2000 data scaling CNX phasing