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Crystal structure of PacII_M1M2S-DNA(m6A)-SAH complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.15 M di-ammonium hydrogen phosphate, 25% PEG 3350, 0.2M Li2SO4, 0.1 M Tris pH 8.5, 20% PEG 3350 (another condition)
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.095 α = 90 b = 121.668 β = 90 c = 129.753 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 80 PIXEL DECTRIS EIGER R 4M 2021-10-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 2.55 49.17 98.84 0.02371 0.03277 0.02317 0.998 18.54 1.6 56313 35.96
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 2.55 2.641 0.319 0.4352 0.319 1 2.71
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7VRU 2.55 49.17 1.34 56005 2766 98.35 0.1835 0.1808 0.1824 0.2368 0.2363 40.24
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 f_dihedral_angle_d 18.9158 f_angle_d 0.9908 f_chiral_restr 0.0532 f_bond_d 0.0083 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10789 Nucleic Acid Atoms 1026 Solvent Atoms 419 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction PHENIX phasing Coot model building HKL-2000 data scaling