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Human PPAR gamma ligand binding domain in complex with MCC555
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.8M Sodium Citrate, 0.1M Hepes (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.252 α = 90 b = 59.812 β = 103.89 c = 117.846 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2008-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 2.1 50 97.9 0.049 15.4 36743 35971
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 2.1 2.18 96 0.137 8.6
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 (All) 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 2PRG 2.1 19.83 36743 34134 1795 97.44 0.19955 0.19955 0.19792 0.2046 0.22945 0.2314 RANDOM 47.845
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] -0.23 -0.02 0.49 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_3_deg 14.347 r_dihedral_angle_4_deg 13.203 r_dihedral_angle_1_deg 5.084 r_angle_refined_deg 1.036 r_angle_other_deg 0.815 r_chiral_restr 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_3_deg 14.347 r_dihedral_angle_4_deg 13.203 r_dihedral_angle_1_deg 5.084 r_angle_refined_deg 1.036 r_angle_other_deg 0.815 r_chiral_restr 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4049 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling