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Crystal structure of the Human TR4 DNA-Binding Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Malonate
Crystal Properties Matthews coefficient Solvent content 1.81 32.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.229 α = 90 b = 32.229 β = 90 c = 128.043 γ = 90
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 2M 2019-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.599 50 99.6 0.9957 21.2 9.1 17222
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.599 1.64 0.933
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DZU 1.599 32.031 15931 860 92.515 0.177 0.1764 0.1852 0.1805 0.1857 16.573
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_dihedral_angle_2_deg 24.006 r_dihedral_angle_3_deg 16.731 r_dihedral_angle_4_deg 15.423 r_dihedral_angle_1_deg 6.741 r_lrange_it 5.352 r_lrange_other 5.332 r_scangle_it 4.192 r_scangle_other 4.192 r_scbond_it 2.715 r_scbond_other 2.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.006 r_dihedral_angle_3_deg 16.731 r_dihedral_angle_4_deg 15.423 r_dihedral_angle_1_deg 6.741 r_lrange_it 5.352 r_lrange_other 5.332 r_scangle_it 4.192 r_scangle_other 4.192 r_scbond_it 2.715 r_scbond_other 2.708 r_mcangle_it 2.475 r_mcangle_other 2.474 r_angle_refined_deg 1.761 r_mcbond_other 1.685 r_mcbond_it 1.683 r_angle_other_deg 1.574 r_nbd_refined 0.231 r_nbd_other 0.231 r_symmetry_nbd_refined 0.197 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.128 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing