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The structure of Deinococcus radiodurans Yqgf
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.1 M MgCl2, 0.1M HEPES (pH 7.0), 15% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2 38.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.07 α = 90 b = 49.38 β = 101.665 c = 33.52 γ = 90
Symmetry Space Group C 1 2 1
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 1.5 27.07 93.7 0.055 26.04 4.5 19580 16.5
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 1.5 1.54 0.132
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 1OVQ 1.50006105724 27.0688711921 1.4025631195 17915 874 95.2064622416 0.194792841433 0.194754700845 0.195 0.19556726321 0.1981 15.6326682596
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 20.6489825135 f_angle_d 1.04268011018 f_chiral_restr 0.0441592537837 f_bond_d 0.0101449670599 f_plane_restr 0.00505225157136
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 943 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XDS data scaling PHASER phasing