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Crystal structure of the MPND-DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG4000, sodium citrate, ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.783 α = 72.583 b = 62.922 β = 89.876 c = 69.085 γ = 89.976
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 2020-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9793 SSRF BL10U2
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 2.47 50 96 0.968 9.5 3.4 21839
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 2.47 2.51 0.894 9.5
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 7YDT 2.47 33.44 20906 1107 95.93 0.246 0.2454 0.2454 0.2536 0.2678 46.658
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] -2.596 -1.187 0.543 -5.688 -1.263 6.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.768 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 14.634 r_lrange_it 6.071 r_lrange_other 6.059 r_dihedral_angle_1_deg 5.691 r_mcangle_it 3.961 r_mcangle_other 3.96 r_scangle_it 3.429 r_scangle_other 3.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.768 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 14.634 r_lrange_it 6.071 r_lrange_other 6.059 r_dihedral_angle_1_deg 5.691 r_mcangle_it 3.961 r_mcangle_other 3.96 r_scangle_it 3.429 r_scangle_other 3.429 r_mcbond_it 2.388 r_mcbond_other 2.388 r_scbond_it 1.979 r_scbond_other 1.979 r_angle_other_deg 1.186 r_angle_refined_deg 1.181 r_nbd_refined 0.185 r_symmetry_nbd_other 0.168 r_nbd_other 0.16 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_nbd_refined 0.113 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2841 Nucleic Acid Atoms 409 Solvent Atoms 161 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing