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Crystal structure of human ERRg LBD in complex with indole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30%(w/v) PEG 5000 MME 0.1M Tris 8.0 0.2M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.371 α = 90 b = 64.371 β = 90 c = 138.422 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2024-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.52 69.21 79.3 0.038 0.039 0.008 1 51.1 18.7 36519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.54 18.7 0.537 0.672 0.394 0.584 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.52 58.37 34626 1804 79.14 0.17152 0.16945 0.1813 0.21184 0.2205 RANDOM 19.763
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] -0.21 -0.21 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 15.913 r_dihedral_angle_3_deg 12.818 r_long_range_B_refined 6.002 r_long_range_B_other 5.836 r_dihedral_angle_1_deg 5.345 r_scangle_other 4.384 r_scbond_it 2.946 r_scbond_other 2.937 r_mcangle_other 2.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 15.913 r_dihedral_angle_3_deg 12.818 r_long_range_B_refined 6.002 r_long_range_B_other 5.836 r_dihedral_angle_1_deg 5.345 r_scangle_other 4.384 r_scbond_it 2.946 r_scbond_other 2.937 r_mcangle_other 2.855 r_mcangle_it 2.853 r_mcbond_it 1.948 r_mcbond_other 1.938 r_angle_refined_deg 1.852 r_angle_other_deg 1.558 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1876 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing