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transcription factor BARHL2 bound to DNA sequences
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PM5 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 2.16 44.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.658 α = 90 b = 47.118 β = 90 c = 72.301 γ = 90
Symmetry Space Group P 21 21 21
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 2021-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976260 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 1.3 47.12 99.7 0.078 0.084 0.032 0.998 10.2 7.1 32926
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 1.3 1.33 94.8 2.156 2.336 0.883 0.264 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 1.3 34.11 31279 1583 99.62 0.18317 0.18169 0.1817 0.21327 0.213 RANDOM 20.917
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] -0.28 0.39 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.302 r_dihedral_angle_4_deg 20.947 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 11.466 r_long_range_B_refined 3.548 r_long_range_B_other 3.547 r_angle_refined_deg 2.536 r_scangle_other 2.058 r_scbond_it 1.378 r_scbond_other 1.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.302 r_dihedral_angle_4_deg 20.947 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 11.466 r_long_range_B_refined 3.548 r_long_range_B_other 3.547 r_angle_refined_deg 2.536 r_scangle_other 2.058 r_scbond_it 1.378 r_scbond_other 1.378 r_angle_other_deg 1.339 r_mcangle_it 1.132 r_mcangle_other 1.131 r_mcbond_it 0.788 r_mcbond_other 0.777 r_chiral_restr 0.213 r_gen_planes_refined 0.02 r_bond_refined_d 0.019 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 529 Nucleic Acid Atoms 486 Solvent Atoms 268 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing