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Dbr1 in complex with 5-mer cleavage product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 15% PEG3350, 0.4 M LiSO4, 0.1 M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.73 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.272 α = 90 b = 143.341 β = 90 c = 214.006 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 PIXEL DECTRIS PILATUS 6M-F 2013-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0000 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 50.12 99 0.02418 0.0342 0.998 20.91 1.9 130333 47.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.175 0.368 0.5205 0.735 2.11
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 5k73 2.1 50.12 2.76 130323 12181 95.86 0.1794 0.1778 0.2092 0.2238 57.8
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 17.2497 f_angle_d 0.9985 f_chiral_restr 0.058 f_bond_d 0.008 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14285 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 394
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction