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Crystal structure of PM54 bound to 10-mer duplex DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal B-DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 25% polyethylene glycol 400, 50 mM MES pH 6.5, 50 mM KCl, 100 mM LiCl and 12 mM spermine
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.43 α = 90 b = 126.688 β = 90 c = 43.387 γ = 90
Symmetry Space Group C 2 2 2
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 2024-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
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 2.1 46.258 100 0.042 0.05 0.027 0.999 16.3 6.2 15329 50.9
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 2.1 2.2 99.9 0.988 1.262 0.774 0.588 1.1 4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 46.258 15328 748 99.909 0.245 0.2427 0.2442 0.2802 0.2818 59.041
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] -2.323 5.06 -2.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 50.997 r_lrange_other 10.416 r_lrange_it 10.412 r_scangle_it 8.579 r_scangle_other 8.577 r_scbond_it 6.183 r_scbond_other 6.183 r_dihedral_angle_other_2_deg 4.507 r_angle_refined_deg 2.434 r_angle_other_deg 0.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 50.997 r_lrange_other 10.416 r_lrange_it 10.412 r_scangle_it 8.579 r_scangle_other 8.577 r_scbond_it 6.183 r_scbond_other 6.183 r_dihedral_angle_other_2_deg 4.507 r_angle_refined_deg 2.434 r_angle_other_deg 0.596 r_nbd_refined 0.287 r_nbtor_refined 0.266 r_nbd_other 0.225 r_symmetry_nbd_other 0.223 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_refined 0.204 r_symmetry_nbtor_other 0.098 r_chiral_restr 0.089 r_gen_planes_refined 0.013 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 808 Solvent Atoms 32 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing