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Structure of Deinococcus radiodurans HerA-ADP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WRW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 289 0.2 M MgCl2, 0.1 M HEPES (pH 7.8), 14% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.011 α = 90 b = 202.869 β = 90 c = 411.852 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 1 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 3.39 102.9 97.5 0.157 7.8 5.4 120020 72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.39 3.46 0.618
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 7WRW 3.40003560509 9.99988280767 1.33473620971 114924 5820 97.5618866515 0.276419459316 0.275648835352 0.2755 0.290776296642 0.29 70
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 20.7214055994 f_angle_d 1.23886909128 f_chiral_restr 0.0800659381304 f_bond_d 0.00848454328183 f_plane_restr 0.00663719683494
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 54976 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 326
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XDS data scaling PHASER phasing