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MmCPDII-DNA complex containing low-dosage, light induced repaired DNA.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 7YC7 initial model was the dark structure of a TR-SFX time-course
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 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.83 α = 90 b = 115.04 β = 90 c = 167.71 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 100 CCD RAYONIX MX225HE 2018-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
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 2.5 49.95 99.9 0.739 4.66 26.53 48931 3.19
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 2.5 2.65 100 0.437
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 7YC7 2.5 49.29 1.36 48859 2425 99.94 0.2198 0.2177 0.2206 0.2587 0.2615
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 20.365 f_angle_d 0.727 f_chiral_restr 0.044 f_plane_restr 0.017 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6932 Nucleic Acid Atoms 1021 Solvent Atoms 556 Heterogen Atoms 165
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC phasing