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Crystal structure of estrogen related receptor-gamma DNA binding domain complexed with Pla2g12b promoter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Sodium malonate pH 6.0, 12% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.403 α = 90 b = 74.434 β = 104.98 c = 111.02 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 PIXEL DECTRIS PILATUS3 6M 2021-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 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 2.2 53.62 99.2 0.084 0.091 0.036 0.994 9.8 6.5 30806
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 2.2 2.27 98.6 0.509 0.557 0.223 0.962 6.1
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 2.2 44.29 29353 1440 98.98 0.22041 0.21859 0.2243 0.26001 0.2689 RANDOM 57.604
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] 8.96 1.2 -1.07 -7.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.662 r_dihedral_angle_3_deg 18.565 r_dihedral_angle_4_deg 14.128 r_dihedral_angle_1_deg 6.826 r_long_range_B_refined 6.478 r_long_range_B_other 6.475 r_scangle_other 4.285 r_scbond_other 3.174 r_scbond_it 3.173 r_angle_refined_deg 1.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.662 r_dihedral_angle_3_deg 18.565 r_dihedral_angle_4_deg 14.128 r_dihedral_angle_1_deg 6.826 r_long_range_B_refined 6.478 r_long_range_B_other 6.475 r_scangle_other 4.285 r_scbond_other 3.174 r_scbond_it 3.173 r_angle_refined_deg 1.651 r_mcangle_it 1.633 r_mcangle_other 1.633 r_angle_other_deg 1.443 r_mcbond_it 0.991 r_mcbond_other 0.988 r_chiral_restr 0.077 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 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 1813 Nucleic Acid Atoms 1382 Solvent Atoms 87 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing