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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 1.97 37.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.7 α = 90 b = 52.776 β = 91.1 c = 65.891 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 2004-05-31 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 2.1 40 97.2 0.062 15582 15141 -3 11.7
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 2.1 2.18 95.4 0.247 1472
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 2.1 19.35 15129 1532 96.8 0.206 0.206 0.2041 0.252 0.2525 RANDOM 26
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] 6.14 -0.86 -2.6 -3.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_scangle_it 2.63 c_mcangle_it 1.8 c_scbond_it 1.8 c_mcbond_it 1.12 c_angle_deg 1.1 c_improper_angle_d 0.67 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_scangle_it 2.63 c_mcangle_it 1.8 c_scbond_it 1.8 c_mcbond_it 1.12 c_angle_deg 1.1 c_improper_angle_d 0.67 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 2197 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 42
Software Software Software Name Purpose X-PLOR model building CNS refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing