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TR-SFX MmCPDII-DNA complex: 10 ns time-point collected in SACLA. Includes 10 ns, dark, and extrapolated structure factors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YDZ 7YDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.6 296 100 mM Sodium Acetate pH 4.6
250 mM ammonium sulfate
4% PEG4000 (w/v)
50 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.53 α = 90 b = 115.71 β = 90 c = 169.28 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 298 CCD MPCCD 2017-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.0875 SACLA BL2
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 2.6 45.23 100 0.985 4.89 247.64 44681
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 2.6 2.62 100 0.493 1.44
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7YDZ 2.7 45.23 39899 1906 99.98 0.2423 0.241 0.2411 0.2667 0.2664
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 20.967 f_angle_d 0.531 f_chiral_restr 0.038 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7028 Nucleic Acid Atoms 1040 Solvent Atoms 221 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction pointless data scaling REFMAC phasing