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transcription factor SATB1 CUTr1 domain in complex with a phosphorothioate DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 50 mM Tris-HCl (pH 8.5), 20% polyethylene glycol monomethyl ether 550 (Sigma-Aldrich), 20% ethylene glycol, and 10 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.17 37.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.32 α = 90 b = 45.32 β = 90 c = 97.862 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2015-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.79 48.94 93.2 0.105 11.6 6.7 19724
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.89 100 0.353 4.8 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2O4A 1.79 19.63 18596 1112 93.29 0.23207 0.22962 0.2356 0.27122 0.2743 RANDOM 38.704
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.336 r_dihedral_angle_4_deg 19.035 r_dihedral_angle_3_deg 15.304 r_long_range_B_refined 5.052 r_long_range_B_other 5.051 r_dihedral_angle_1_deg 4.651 r_mcangle_it 3.295 r_mcangle_other 3.293 r_scangle_other 3.034 r_mcbond_other 2.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.336 r_dihedral_angle_4_deg 19.035 r_dihedral_angle_3_deg 15.304 r_long_range_B_refined 5.052 r_long_range_B_other 5.051 r_dihedral_angle_1_deg 4.651 r_mcangle_it 3.295 r_mcangle_other 3.293 r_scangle_other 3.034 r_mcbond_other 2.023 r_mcbond_it 2.022 r_scbond_it 1.833 r_scbond_other 1.832 r_angle_other_deg 1.269 r_angle_refined_deg 1.224 r_chiral_restr 0.062 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d 0.002 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 1346 Nucleic Acid Atoms 471 Solvent Atoms 69 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing