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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 2.05 39.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.91 α = 90 b = 54.516 β = 91.89 c = 66.543 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 2011-02-08 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 1.6 50 99.6 0.066 3.6 36814 36676 -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 99.9 3.3 3644
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 1.6 20 32975 3667 99.45 0.22618 0.22415 0.2336 0.24403 0.2509 RANDOM 19.196
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] 0.87 -0.05 -0.18 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.817 r_dihedral_angle_4_deg 16.739 r_dihedral_angle_3_deg 11.568 r_dihedral_angle_1_deg 4.221 r_scangle_it 1.578 r_angle_refined_deg 1.003 r_scbond_it 0.939 r_angle_other_deg 0.775 r_mcangle_it 0.678 r_mcbond_it 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.817 r_dihedral_angle_4_deg 16.739 r_dihedral_angle_3_deg 11.568 r_dihedral_angle_1_deg 4.221 r_scangle_it 1.578 r_angle_refined_deg 1.003 r_scbond_it 0.939 r_angle_other_deg 0.775 r_mcangle_it 0.678 r_mcbond_it 0.35 r_chiral_restr 0.042 r_mcbond_other 0.04 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2150 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 42
Software Software Software Name Purpose CrystalClear data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing