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Crystal structure of estrogen related receptor-alpha DNA binding domain complexed with MPC1 promoter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8IFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M potassium chloride, 0.05M HEPES pH 7.6, 29% v/v pentaerythritol propxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.021 α = 90 b = 66.021 β = 90 c = 365.843 γ = 90
Symmetry Space Group P 43 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 2021-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9792 SSRF BL18U1
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 2.79 91.46 98.8 0.148 0.152 0.032 0.998 16.4 22 21207
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 2.79 2.94 100 2.279 2.329 0.477 0.872 23.4
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 2.79 91.46 20014 1088 98.71 0.22156 0.21857 0.2244 0.27962 0.2812 RANDOM 81.126
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] 3.42 3.42 -6.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.714 r_dihedral_angle_4_deg 19.5 r_dihedral_angle_3_deg 19.191 r_long_range_B_refined 14.538 r_long_range_B_other 14.537 r_mcangle_it 13.682 r_mcangle_other 13.679 r_scangle_other 13.634 r_scbond_it 9.283 r_scbond_other 9.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.714 r_dihedral_angle_4_deg 19.5 r_dihedral_angle_3_deg 19.191 r_long_range_B_refined 14.538 r_long_range_B_other 14.537 r_mcangle_it 13.682 r_mcangle_other 13.679 r_scangle_other 13.634 r_scbond_it 9.283 r_scbond_other 9.28 r_mcbond_other 9.195 r_mcbond_it 9.194 r_dihedral_angle_1_deg 8.064 r_angle_refined_deg 1.86 r_angle_other_deg 1.411 r_chiral_restr 0.119 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 2806 Nucleic Acid Atoms 1136 Solvent Atoms 49 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement Aimless data scaling autoPROC data reduction PHASER phasing