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transcription factor BARHL2 bound to TAAAT DNA sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A01 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 PEG 4000, sodium malonate, sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.5 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.015 α = 90 b = 134.298 β = 92.6 c = 65.625 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 2021-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9677 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 2.33 46.95 96.6 0.154 0.167 0.063 0.996 8.8 7.2 27918
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 2.33 2.41 72.3 2.965 3.22 1.233 0.179 6.6
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 2.4 46.95 24935 1251 99.24 0.23118 0.22863 0.2329 0.28042 0.284 RANDOM 47.849
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] -2.8 1.68 4 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.925 r_dihedral_angle_4_deg 22.749 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_1_deg 8.681 r_long_range_B_refined 3.98 r_long_range_B_other 3.98 r_angle_refined_deg 2.111 r_scangle_other 1.782 r_mcangle_it 1.632 r_mcangle_other 1.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.925 r_dihedral_angle_4_deg 22.749 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_1_deg 8.681 r_long_range_B_refined 3.98 r_long_range_B_other 3.98 r_angle_refined_deg 2.111 r_scangle_other 1.782 r_mcangle_it 1.632 r_mcangle_other 1.631 r_angle_other_deg 1.113 r_scbond_it 1.107 r_scbond_other 1.107 r_mcbond_it 0.991 r_mcbond_other 0.987 r_chiral_restr 0.174 r_bond_refined_d 0.017 r_gen_planes_refined 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 2599 Nucleic Acid Atoms 1942 Solvent Atoms 261 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing