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Estrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 9% PEG 20K 0.1M MES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.69 66.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.81 α = 90 b = 203.81 β = 90 c = 53.46 γ = 120
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 MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 2.6 50 98.8 0.064 9.5 25371 25066 -3 -3
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) 2.6 2.64 84.9 0.403 3.2
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 2GP7 2.6 45.74 25372 25065 764 98.79 0.233 0.233 0.232 0.2192 0.257 0.2505 RANDOM 44.602
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] -0.86 -0.43 -0.86 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.503 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_4_deg 14.94 r_dihedral_angle_1_deg 5.576 r_scangle_it 1.911 r_scbond_it 1.222 r_angle_refined_deg 1.215 r_mcangle_it 0.939 r_angle_other_deg 0.733 r_mcbond_it 0.609
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.503 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_4_deg 14.94 r_dihedral_angle_1_deg 5.576 r_scangle_it 1.911 r_scbond_it 1.222 r_angle_refined_deg 1.215 r_mcangle_it 0.939 r_angle_other_deg 0.733 r_mcbond_it 0.609 r_nbd_refined 0.23 r_symmetry_vdw_other 0.198 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.178 r_nbd_other 0.167 r_xyhbond_nbd_refined 0.149 r_mcbond_other 0.146 r_nbtor_other 0.088 r_chiral_restr 0.06 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 r_symmetry_hbond_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3760 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 21
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection