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The structure of G.kaustophilus T-1 ScoC-17bp dsDNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 3350 and 0.3 M Magnesium formate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.634 α = 89.773 b = 70.546 β = 81.625 c = 95.468 γ = 60.911
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 EIGER X 16M 2019-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.8 48.48 98.3 0.08 0.09 0.05 0.93 6.3 3.8 37515 63.56
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 2.8 2.9 0.66 0.77 0.39 0.51 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 48.48 1.96 37284 1803 98.1 0.2312 0.2282 0.2307 0.2931 0.2918 69.89
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 29.9005 f_angle_d 1.1908 f_chiral_restr 0.0583 f_bond_d 0.011 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5936 Nucleic Acid Atoms 2848 Solvent Atoms 49 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction Aimless data scaling PHENIX phasing