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Crystal structure of the C-terminal dimerization domain of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RNX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Sodium Citrate Tribasic pH 4.5, 0.2 M Lithium sulfate, 46% w/v PEG 400
Crystal Properties Matthews coefficient Solvent content 1.88 34.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.91 α = 90 b = 76.8 β = 90 c = 102.32 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 PILATUS3 2M 2016-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9660 ESRF MASSIF-1
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 1.41 61.42 92.4 0.037 17.5 4.9 73609 20.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.43 0.49
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6RNX 1.41 60 1.37 73601 4002 92.38 0.1962 0.1947 0.2237 0.2455 RANDOM 35.99
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 5.4147 f_angle_d 1.533 f_chiral_restr 0.0982 f_bond_d 0.018 f_plane_restr 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3667 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction autoPROC data scaling MOLREP phasing