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The structure of Deinococcus radiodurans RuvC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 289 0.2 M MgCl2, 0.1M HEPES (pH 7.8), 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.2 α = 90 b = 72.77 β = 90 c = 112.3 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 CCD ADSC QUANTUM 315r 2021-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 27.71 91.2 0.131 13.4 4 9594 57.4767212532
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.79 0.722
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 4EP4 2.75016129042 27.705522236 1.3549347961 8220 434 88.7976666307 0.275071348481 0.273390366557 0.2778 0.30581259884 0.3067 63.2475739321
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 20.8807603012 f_angle_d 0.757308413906 f_chiral_restr 0.045050258135 f_bond_d 0.00436575177774 f_plane_restr 0.00387810933674
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing