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Transcription factor BARHL2 homodimer with spacing two bp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PM5 monomeric model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Sodium Cacodilate buffer (pH 6.5),
PEG (4000)
5% butanol
Crystal Properties Matthews coefficient Solvent content 2.62 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.335 α = 90 b = 63.169 β = 111.72 c = 51.323 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M-F 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.619920 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 1.98 47.68 98.2 0.083 0.092 0.039 0.997 4.6 5.5 18391
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 1.98 2.03 88.6 3.426 3.821 1.656 0.414 4.9
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 1.98 47.68 17365 905 97.49 0.23476 0.23269 0.2389 0.27262 0.2765 RANDOM 73.212
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] 1.86 1.66 2.56 -4.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.77 r_long_range_B_refined 9.69 r_long_range_B_other 9.684 r_mcangle_it 7.667 r_mcangle_other 7.665 r_dihedral_angle_2_deg 7.576 r_scangle_other 7.337 r_dihedral_angle_1_deg 6.178 r_mcbond_it 5.439 r_mcbond_other 5.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.77 r_long_range_B_refined 9.69 r_long_range_B_other 9.684 r_mcangle_it 7.667 r_mcangle_other 7.665 r_dihedral_angle_2_deg 7.576 r_scangle_other 7.337 r_dihedral_angle_1_deg 6.178 r_mcbond_it 5.439 r_mcbond_other 5.436 r_scbond_it 5.157 r_scbond_other 5.155 r_angle_refined_deg 2.174 r_angle_other_deg 0.571 r_chiral_restr 0.084 r_gen_planes_refined 0.01 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1076 Nucleic Acid Atoms 650 Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing