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Crystal structure of human ERRg LBD in complex with 5-nitroindole
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 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.095 α = 90 b = 64.095 β = 90 c = 137.526 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 2015-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 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 1.8 68.76 86.8 0.071 0.072 0.015 0.999 27.8 21.1 23843
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 1.8 1.84 49.3 0.486 0.515 0.164 0.935 9.1
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 1.8 58.1 22585 1196 86.67 0.1756 0.17319 0.1848 0.22407 0.2371 RANDOM 27.908
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] -0.78 -0.78 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.224 r_dihedral_angle_4_deg 18.104 r_dihedral_angle_3_deg 14.738 r_long_range_B_refined 7.399 r_long_range_B_other 7.384 r_scangle_other 6.092 r_dihedral_angle_1_deg 5.049 r_scbond_it 3.986 r_scbond_other 3.977 r_mcangle_other 3.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.224 r_dihedral_angle_4_deg 18.104 r_dihedral_angle_3_deg 14.738 r_long_range_B_refined 7.399 r_long_range_B_other 7.384 r_scangle_other 6.092 r_dihedral_angle_1_deg 5.049 r_scbond_it 3.986 r_scbond_other 3.977 r_mcangle_other 3.424 r_mcangle_it 3.423 r_mcbond_it 2.438 r_mcbond_other 2.431 r_angle_refined_deg 1.64 r_angle_other_deg 1.446 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 172 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing