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transcription factor BARHL2 homodimer with spacing four bp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PM5 monomerik model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.05M Sodium Cacodilate buffer (pH 6.5),
PEG (4000), PEG(200)
Crystal Properties Matthews coefficient Solvent content 3.84 67.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.955 α = 90 b = 159.955 β = 90 c = 159.955 γ = 90
Symmetry Space Group I 21 3
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-F 2021-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97626 ESRF ID23-1
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 3.26 46.17 99.3 0.179 0.184 0.041 0.995 8.7 21.5 10697
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 3.26 3.52 96.9 5.142 5.28 1.171 0.204 19.6
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 3.26 43 10173 521 99.27 0.20067 0.19764 0.2034 0.25246 0.2511 RANDOM 175.88
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.385 r_long_range_B_other 23.382 r_scangle_other 19.362 r_dihedral_angle_3_deg 18.524 r_mcangle_other 17.935 r_mcangle_it 17.929 r_scbond_it 13.03 r_scbond_other 13.027 r_mcbond_it 12.373 r_mcbond_other 12.368
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.385 r_long_range_B_other 23.382 r_scangle_other 19.362 r_dihedral_angle_3_deg 18.524 r_mcangle_other 17.935 r_mcangle_it 17.929 r_scbond_it 13.03 r_scbond_other 13.027 r_mcbond_it 12.373 r_mcbond_other 12.368 r_dihedral_angle_2_deg 10.338 r_dihedral_angle_1_deg 5.812 r_angle_refined_deg 2.297 r_angle_other_deg 0.562 r_chiral_restr 0.091 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 1959 Nucleic Acid Atoms 1107 Solvent Atoms 6 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing